Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The relationships of groups of organisms as reflected by their genetic makeup.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
A species of fresh-water, flagellated EUKARYOTES in the phylum EUGLENIDA.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The joining of RNA from two different genes. One type of trans-splicing is the "spliced leader" type (primarily found in protozoans such as trypanosomes and in lower invertebrates such as nematodes) which results in the addition of a capped, noncoding, spliced leader sequence to the 5' end of mRNAs. Another type of trans-splicing is the "discontinuous group II introns" type (found in plant/algal chloroplasts and plant mitochondria) which results in the joining of two independently transcribed coding sequences. Both are mechanistically similar to conventional nuclear pre-mRNA cis-splicing. Mammalian cells are also capable of trans-splicing.
The functional hereditary units of FUNGI.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The functional hereditary units of PLANTS.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A class of EUKARYOTA (traditionally algae), characterized by biflagellated cells and found in both freshwater and marine environments. Pigmentation varies but only one CHLOROPLAST is present. Unique structures include a nucleomorph and ejectosomes.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.
Components of ribosomal RNA that undergo auto-catalyzed molecular rearrangements of their RNA sequence.
A nuclear RNA-protein complex that plays a role in RNA processing. In the nucleoplasm, the U2 snRNP along with other small nuclear ribonucleoproteins (U1, U4-U6, and U5) assemble into SPLICEOSOMES that remove introns from pre-mRNA by splicing. The U2 snRNA forms base pairs with conserved sequence motifs at the branch point, which associates with a heat- and RNAase-sensitive factor in an early step of splicing.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
A genus of ciliate protozoa commonly used in genetic, cytological, and other research.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Use for nucleic acid precursors in general or for which there is no specific heading.
A free-living soil amoeba pathogenic to humans and animals. It occurs also in water and sewage. The most commonly found species in man is NAEGLERIA FOWLERI which is the pathogen for primary amebic meningoencephalitis in primates.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
A phylum of unicellular flagellates of ancient eukaryotic lineage with unclear taxonomy. They lack a CELL WALL but are covered by a proteinaceous flexible coat, the pellicle, that allows the cell to change shape. Historically some authorities considered them to be an order of protozoa and others classed them as ALGAE (some members have CHLOROPLASTS and some don't).
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Plant cell inclusion bodies that contain the photosynthetic pigment CHLOROPHYLL, which is associated with the membrane of THYLAKOIDS. Chloroplasts occur in cells of leaves and young stems of plants. They are also found in some forms of PHYTOPLANKTON such as HAPTOPHYTA; DINOFLAGELLATES; DIATOMS; and CRYPTOPHYTA.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.
A plant division. They are simple plants that lack vascular tissue and possess rudimentary rootlike organs (rhizoids). Like MOSSES, liverworts have alternation of generations between haploid gamete-bearing forms (gametophytes) and diploid spore-bearing forms (sporophytes).
The functional hereditary units of protozoa.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The internal fragments of precursor proteins (INternal proTEINS) that are autocatalytically removed by PROTEIN SPLICING. The flanking fragments (EXTEINS) are ligated forming mature proteins. The nucleic acid sequences coding for inteins are considered to be MOBILE GENETIC ELEMENTS. Inteins are composed of self-splicing domains and an endonuclease domain which plays a role in the spread of the intein's genomic sequence. Mini-inteins are composed of the self-splicing domains only.
A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
An order of CRENARCHAEOTA comprised of rod, disc, or spherical shaped, nonseptate, anaerobic, extreme thermophiles and found in solfataric hot waters, mud holes, and superheated submarine environments.
Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.
The genetic complement of MITOCHONDRIA as represented in their DNA.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Genotypic differences observed among individuals in a population.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
The genetic complement of a plant (PLANTS) as represented in its DNA.
Deoxyribonucleic acid that makes up the genetic material of plants.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
A genus of EUKARYOTES, in the phylum EUGLENIDA, found mostly in stagnant water. Characteristics include a pellicle usually marked by spiral or longitudinal striations.

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (1/9869)

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.  (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (2/9869)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.  (+info)

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (3/9869)

Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus.  (+info)

Alterations in the conserved SL1 trans-spliced leader of Caenorhabditis elegans demonstrate flexibility in length and sequence requirements in vivo. (4/9869)

Approximately 70% of mRNAs in Caenorhabditis elegans are trans spliced to conserved 21- to 23-nucleotide leader RNAs. While the function of SL1, the major C. elegans trans-spliced leader, is unknown, SL1 RNA, which contains this leader, is essential for embryogenesis. Efforts to characterize in vivo requirements of the SL1 leader sequence have been severely constrained by the essential role of the corresponding DNA sequences in SL1 RNA transcription. We devised a heterologous expression system that circumvents this problem, making it possible to probe the length and sequence requirements of the SL1 leader without interfering with its transcription. We report that expression of SL1 from a U2 snRNA promoter rescues mutants lacking the SL1-encoding genes and that the essential embryonic function of SL1 is retained when approximately one-third of the leader sequence and/or the length of the leader is significantly altered. In contrast, although all mutant SL1 RNAs were well expressed, more severe alterations eliminate this essential embryonic function. The one non-rescuing mutant leader tested was never detected on messages, demonstrating that part of the leader sequence is essential for trans splicing in vivo. Thus, in spite of the high degree of SL1 sequence conservation, its length, primary sequence, and composition are not critical parameters of its essential embryonic function. However, particular nucleotides in the leader are essential for the in vivo function of the SL1 RNA, perhaps for its assembly into a functional snRNP or for the trans-splicing reaction.  (+info)

Promoter and exon-intron structure of the protein kinase C gene from the marine sponge Geodia cydonium: evolutionary considerations and promoter activity. (5/9869)

We report the gene structure of a key signaling molecule from a marine sponge, Geodia cydonium. The selected gene, which codes for a classical protein kinase C (cPKC), comprises 13 exons and 12 introns; the introns are, in contrast to those found in cPKC from higher Metazoa, small in size ranging from 93 nt to 359 nt. The complete gene has a length of 4229 nt and contains exons which encode the characteristic putative regulatory and catalytic domains of metazoan cPKCs. While in the regulatory domain only one intron is in phase 0, in the catalytic domain most introns are phase 0 introns, suggesting that the latter only rarely undergo module duplication. The 5'-flanking sequence of the sponge cPKC gene contains a TATA-box like motif which is located 35-26 nt upstream from the start of the longest sequenced cDNA. This 5'-flanking sequence was analyzed for promoter activity. The longest fragment (538 nt) was able to drive the expression of luciferase in transient transfections of NIH 3T3 fibroblasts; the strong activity of the sponge promoter was found to be half the one displayed by the SV40 reference promoter. Deletion analysis demonstrates that the AP4 site and the GC box which is most adjacent to the TATA box are the crucial elements for maximal promoter activity. The activity of the promoter is not changed in 3T3 cells which are kept serum starved or in the presence of a phorbol ester. In conclusion, these data present the phylogenetically oldest cPKC gene which contains in the 5'-flanking region a promoter functional in the heterologous mammalian cell system.  (+info)

Interleukin-18 binding protein: a novel modulator of the Th1 cytokine response. (6/9869)

An interleukin-18 binding protein (IL-18BP) was purified from urine by chromatography on IL-18 beads, sequenced, cloned, and expressed in COS7 cells. IL-18BP abolished IL-18 induction of interferon-gamma (IFNgamma), IL-8, and activation of NF-kappaB in vitro. Administration of IL-18BP to mice abrogated circulating IFNgamma following LPS. Thus, IL-18BP functions as an inhibitor of the early Th1 cytokine response. IL-18BP is constitutively expressed in the spleen, belongs to the immunoglobulin superfamily, and has limited homology to the IL-1 type II receptor. Its gene was localized on human chromosome 11q13, and no exon coding for a transmembrane domain was found in an 8.3 kb genomic sequence. Several Poxviruses encode putative proteins highly homologous to IL-18BP, suggesting that viral products may attenuate IL-18 and interfere with the cytotoxic T cell response.  (+info)

The stability and fate of a spliced intron from vertebrate cells. (7/9869)

Introns constitute most of the length of typical pre-mRNAs in vertebrate cells. Thus, the turnover rate of introns may significantly influence the availability of ribonucleotides and splicing factors for further rounds of transcription and RNA splicing, respectively. Given the importance of intron turnover, it is surprising that there have been no reports on the half-life of introns from higher eukaryotic cells. Here, we determined the stability of IVS1Cbeta1, the first intron from the constant region of the mouse T-cell receptor-beta, (TCR-beta) gene. Using a tetracycline (tet)-regulated promoter, we demonstrate that spliced IVS1Cbeta1 and its pre-mRNA had half-lives of 6.0+/-1.4 min and 3.7+/-1.0 min, respectively. We also examined the half-lives of these transcripts by using actinomycin D (Act.D). Act.D significantly stabilized IVS1Cbeta1 and its pre-mRNA, suggesting that Act.D not only blocks transcription but exerts rapid and direct posttranscriptional effects in the nucleus. We observed that in vivo spliced IVS1Cbeta1 accumulated predominantly as lariat molecules that use a consensus branchpoint nucleotide. The accumulation of IVS1Cbeta1 as a lariat did not result from an intrinsic inability to be debranched, as it could be debranched in vitro, albeit somewhat less efficiently than an adenovirus intron. Subcellular-fractionation and sucrose-gradient analyses showed that most spliced IVS1Cbeta1 lariats cofractionated with pre-mRNA, but not always with mRNA in the nucleus. Some IVS1Cbeta1 also appeared to be selectively exported to the cytoplasm, whereas TCR-beta pre-mRNA remained in the nucleus. This study constitutes the first detailed analysis of the stability and fate of a spliced nuclear intron in vivo.  (+info)

Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. (8/9869)

Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.  (+info)

While the role of group I and group II intron-encoded proteins in homing has been well defined, the function of these proteins in intron dissemination to new sites remains the subject of intense study. These mobile introns, their intron-encoded proteins, and the mechanisms by which mobility occurs are the subject of this chapter. Although transition metals are not required for colicin DNase activity, it is likely that they play a stabilizing role related to the membrane translocation that must occur for colicins biological function. These data lend credence to the idea that the HNH domain, like the GIY-YIG domain, is an endonu clease cassette that can become associated with other protein domains to form multifunctional proteins. The open reading frames (ORFs) specifying group II intron-encoded proteins, when present, are located in the loop region of the structural domain IV, with most of the coding sequence outside the intron catalytic core. Of the three activities of the group II intron-encoded
Group II Self-Splicing Introns. -pre-rRNA of fungal and plant mitochondria -majority of chloroplast introns -several classes -require Mg 2+ -no cofactor. Domain Structure of a Group II Intron. A. 5 exon. 3 exon. Chemistry of Group II Self-Splicing. 1st step. 2nd step. lariat. Slideshow 3387240 by guang
Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics ...
TY - JOUR. T1 - Intron size, abundance, and distribution within untranslated regions of genes. AU - Hong, Xin. AU - Scofield, Douglas G.. AU - Lynch, Michael. PY - 2006/12. Y1 - 2006/12. N2 - Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species, Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5′ UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5′ UTRs than in CDSs. Introns in 5′ UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5′ UTR-CDS boundary. We propose a mechanistic explanation for the existence of ...
Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. However, the presence of these introns in eukaryotes and absence in prokaryotes created a debate about the time in which these introns appeared. Two theories arose: the introns early theory and the introns late theory. Supporters of the introns early theory believed that introns and RNA splicing were the relics of the RNA world and therefore both prokaryotes and eukaryotes had introns in the beginning. However, prokaryotes eliminated their introns in order to obtain a higher efficiency, while eukaryotes retained the introns and the genetic plasticity of the ancestors. On the other hand, supporters of the introns late theory ...
The object isnt able to load since the IDs are different. Same is the case with exons and transcripts ids. Upon looking into the .ctab files, the exons, introns, transcripts differ across Control- Sample. But are same across the 3 controls. And they are same across the 5 samples. It is like so- Controls: exon 442247, introns 366654, transcripts 181466. Samples: exon 686514, introns 416565, transcripts 247538. The exons, introns, transcripts differ only between the two conditions. Hence, I am not able to progress from here. Can anyone please help me with as to why this is occuring? Why would the exons, introns, transcripts id be different for control & sample, since both control and sample RNA are collected from human patients. Please add a note on how I can solve this issue.. Any help is much appreciated.. ...
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about Alamut. We are very pleased with Alamut since it conveniently streamlines post-sequencing analyses of detected variants. We value the programme user friendliness and its all-in one approach to variant analysis.. PROF. MILAN MACEK Jr. M.D. Ph.D ...
The objective of this study was primarily to determine the structure and biochemical characteristics of the NmeGp1Sd in order to gain a deeper insight into the evolution of metazoan Nme proteins and their functions.. Sponge Group I Nme genes are intron-rich and these introns are relatively short. The same has been found for introns in several other sponge genes [42, 43] and recently in A. queenslandica genome where median intron size is 80 bp [32]. The fourth intron (Figure 1) is likely the most ancient because it is also found in a choanoflagellate Group I Nme homolog. We conclude that the ancestral metazoan Group I Nme gene was intron-rich and probably had all four introns that are still present in most extant basal metazoan homologs. The ancestral gene structure is also well preserved in vertebrate homologs with three out of four introns present. D. melanogaster has only one of the ancestral introns and C. elegans lost all ancestral introns and gained two new ones which likely reflect ...
Introns may be lost or gained over evolutionary time, as shown by many comparative studies of orthologous genes. Subsequent analyses have identified thousands of examples of intron loss and gain events, and it has been proposed that the emergence of eukaryotes, or the initial stages of eukaryotic evolution, involved an intron invasion.[32] Two definitive mechanisms of intron loss, Reverse Transcriptase-Mediated Intron Loss (RTMIL) and genomic deletions, have been identified, and are known to occur.[33] The definitive mechanisms of intron gain, however, remain elusive and controversial. At least seven mechanisms of intron gain have been reported thus far: Intron Transposition, Transposon Insertion, Tandem Genomic Duplication, Intron Transfer, Intron Gain during Double-Strand Break Repair (DSBR), Insertion of a Group II Intron, and Intronization. In theory it should be easiest to deduce the origin of recently gained introns due to the lack of host-induced mutations, yet even introns gained ...
Many functional RNAs are required to fold into specific three-dimensional structures. A fundamental property of RNA is that its secondary structure and even some tertiary contacts are highly stable, which gives rise to independent modular RNA motifs and makes RNAs prone to adopting misfolded intermediates. Consequently, in addition to stabilizing the native structure relative to the unfolded species (defined here as stability), RNAs are faced with the challenge of stabilizing the native structure relative to alternative structures (defined as structural specificity). How RNAs have evolved to overcome these challenges is incompletely understood. Self-splicing group I introns have been used to study RNA structure and folding for decades. Among them, the Tetrahymena intron was the first discovered and has been studied extensively. In this work, we found that a version of the intron that was generated by in vitro selection for enhanced stability also displayed enhanced specificity against a stable ...
Group II introns are large metallo-ribozymes that use divalent metal ions in folding and catalysis. The 3-terminal domain 6 contains a conserved adenosine whose 2-OH acts as the nucleophile in the first splicing step. In the hierarchy of folding, D6 binds last into the active site. In order to investigate and understand the folding process to the catalytically active intron structure, it is important to know the individual binding affinities of Mg2+ ions to D6. We recently studied the solution structure of a 27 nucleotide long domain 6 (D6-27) from the mitochondrial yeast group II intron Sc.ai5, identifying also five Mg2+ binding sites including the one at the 5-terminal phosphate residues. Mg2+ coordination to the 5-terminal di- and triphosphate groups is strongest (e.g., log KA,TP = 4.55 ± 0.10) and could be evaluated here in detail for the first time. The other four binding sites within D6-27 are filled simultaneously (e.g., log KA,BR = 2.38 ± 0.06) and thus compete for the free Mg2+ ...
The exon/intron organisation of homologous nuclear genes was compared in several yeast species. CLUSTALX multiple alignments were performed to verify the degree of conservation of the homologues and to reconstruct a virtual (scaffold) gene, exhibiting the probable ancestral intron arrangement. Intron position was defined at the nucleotide level making it possible to determine whether the intron is at an identical position (same codon and same phase) or not in the homologues.. In the cases herein illustrated, some intron positions were found divergent in homologues sharing a high degree of sequence conservation, suggesting that these positions may result either from intron sliding or intron gain events [Bon et al., 2003]. Intron sliding is defined as the relocation of a pre-existing intron over short distances in the course of gene evolution [Rogozin et al., 2000, Trends Genet., 16, 430-432]. Although it is now admitted that intron sliding by one or two bases is a real phenomenon, it remains ...
This site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Introns present special problems for the annotation of eukaryotic genomes. Splice sites are information-poor, and their recognition by the splicing apparatus is highly context-dependent and regulated, making identification by computational gene prediction programs a challenge. At present we do not understand splice site context well enough to predict which potential splice sites will be used, and thus how the genomic sequences will be expressed. Understanding the how and why of introns will require genome level information about splicing. One element of this will involve understanding splicing patterns and how they are regulated globally. Another element will involve understanding how splicing patterns change during evolution. To begin we study yeast, since it has the simplest known eukaryotic genome. In these pages we have listed known spliceosomal introns in the yeast genome and documented the ...
Recording during rehearsal, december 2018 Reboot by de Introns Recordings 2016 with former member Theo on the drums. de Introns by de Introns
The wide, but scattered distribution of group I introns in nature is a result of two processes; the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. Reversal of the group I intron
Most metazoan genes have multiple exons that must be carefully excised (from the pre-mRNA) and then ligated (to form the mRNA). This RNA splicing occurs in the nucleus, and upon its completion the mRNA is exported to the cytoplasm for translation. Exon definition complexes and spliceosomes begin to assemble during transcription. Some of these complexes interact with RNAP IIs CTD, and some introns are thus excised before transcription has even terminated.. There is no apparent order in which introns get spliced). Introns do no excise in any particular order, and active transcription (or its termination) is not needed for splicing to occur. However, the rate of transcription elongation through an intron can strongly affect what splice sites are chosen and thus indirectly couple transcription and splicing. Exon definition complexes and spliceosomes begin assembling during RNA synthesis; interaction with RNAP IIs CTD leads to excision of some introns before transcription has even ...
Isolation and Characterization of Functional Tripartite Group II Introns Using a Tn5-Based Genetic Screen. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Group II Introns: Structure, Function, and Catalysis - CHEMICAL BIOLOGY - reflects the multidimensional character of chemical biology, focusing in particular on the fundamental science of biological structures and systems, the use of chemical and biological techniques to elucidate
We read with great interest the recent paper by Beer and Sahin-Tóth1 addressing the missing heritability observed in approximately 60% of German cases of chronic pancreatitis.2 These authors opined that discovery studies tend to focus on exons and exon-intron boundaries and may thus miss many intronic variants.1 This premise seems eminently reasonable, given the generally much larger size of intronic sequences as compared with the coding sequences of protein-coding genes. However, there is a trade-off here. On the one hand, larger sequence size means larger target size for mutation, and hence the greater the number of mutations that could be missed if intronic sequences were not screened. On the other hand, to be of pathological significance, an intronic mutation must either create a new functional splicing donor or acceptor site or alternatively impact a functional sequence motif responsible for regulating splicing (eg, an intronic splicing enhancer), which depends upon many additional ...
There are many unanswered questions about introns. It is unclear whether introns serve some specific function, or whether they are selfish DNA which reproduces itself as a parasite.[5] Recent studies of entire eukaryotic genomes have now shown that the lengths and density (introns/gene) of introns varies considerably between related species. There are four or five different kinds of intron. Some introns represent mobile genetic elements (transposons). Alternative splicing of introns within a gene allows a variety of protein isoforms from a single gene. Thus multiple related proteins can be generated from a single gene and a single precursor mRNA transcript. The control of alternative RNA splicing is performed by complex network of signalling molecules. In humans, ~95% of genes with more than one exon are alternatively spliced.[6] ...
For each BAM, we use samtools to retrieve the reads in the region(s)) of interest. The reads are then filtered with samjs (https://github.com/lindenb/jvarkit/wiki/SamJS) to only keep the reads carrying an intron-exon junction at the desired location(s). Basically, the javascript-based filter loops over the CIGAR string of the read, computes the genomic interval skipped when the cigar operator is a deletion or a skipped region/intron. The read is printed if it describes the new intron-exon junction ...
We compared the expression patterns and functional annotations of genes with and without 5UIs. We found that the most highly expressed genes reveal a strong enrichment for having short 5UIs as opposed to having either no 5UIs or longer 5UIs. This effect was specific to genes with the highest expression levels and no relationship between length and expression level was observed for genes with intermediate or long introns (Figure2d). These results are contrary to the energetic cost model [23], which predicts that genes with no 5UIs will be more highly represented among those with the highest expression levels. Because expression reflects both production and degradation rates of mRNAs, our results suggest that short 5UIs tend to either enhance transcription or stabilize mature mRNAs.. The prevalence and the significance of these intron-dependent mechanisms of transcriptional enhancement at a genome-wide level are poorly understood in mammalian systems. There are a few examples in mammals of ...
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene.[1][2]The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts.[3] Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that followstranscription and precedes translation ...
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene.[1][2]The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts.[3] Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that followstranscription and precedes translation ...
[Ive combined all the previous intron entries together to make it easier to read. However, did not have the time to thoroughly edit, so some parts might seem a little repetitive.] Since I will be discussing introns, let me begin with a few points of clarification. First, I will be focusing on introns found in…
Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems.
The sections of m RNA which do not code for translation of a polypeptide are called introns.. As the m RNA readies itself to leave the nucleus, enzymes cut out and remove the introns.. …. These are cut out of the mRNA and kept in the nucleus.. Exons: Sections of mRNA containing the code to synthesize a protein... ...
a Overview of MASP1 mutations. Exons and introns are indicated by circles with numbers and thin lines, respectively. The localization of mutations identified in
Then there are introns, which are often considered DNA spacers with a possible error-checking function, inside the DNA strand. Introns do not code for proteins. Some species have a lot of introns in total DNA. Exons are what is leftover in the DNA strand when the introns have been peeled off. Exons can be less than 60% of the total DNA. It is likely the introns are for a reason, but they do represent a change that is kind of like fiber filling, sort of a do-nothing or copy-proofing addition ...
Usually the primary challenge that follows the sequencing of anything from a small segment of DNA to a complete genome is to establish where the location functional elements such as: genes (intron/exon boundaries) promoters, terminators etc DNA sequences that may potentially encode proteins are called Open Reading Frames (ORFs) The situation in prokaryotes is relatively straightforward since scarcely any eubacterial and archaeal genes contain introns
Phylogenetic analysis of 71 group II intron ORFs. A maximum likelihood analysis of the amino acid sequence for 71 ORFs suggests the cox1 ORF718 of the marine ce
Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
Berget, S.M., Sharp, P.A. (1977) A spliced sequence at the 5′-terminus of adenovirus late mRNA. Brookhaven Symp Biol, 29:332-44.. Berk, A.J., Sharp, P.A. (1977) Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12(3): 721-32.. Chow, L.T., Roberts, J.M., Lewis, J.B., Broker, T.R. (1977) A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA:DNA hybrids. Cell, 11(4): 819-36.. Gibbs, W.W. (2003) The unseen genome: gems among the junk. Scientific American 289(5):26-33.. Hooks, K. B., Delneri, D. & Grifths-Jones, S. (2014) Intron evolution in Saccharomycetaceae. Genome Biol. Evol. 6, 2543-2556.. Kabat, J.L., Barberan-Soler, S., McKenna, P., Clawson, H., Farrer, T., and Zahler, A.M. (2006) Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes. PLoS Computational Biology 2(7):734-747.. Kiss, T. and Filipowicz, W. (1995) Genes and Development ...
The conventional model for splicing involves excision of each intron in one piece; we demonstrate this inaccurately describes splicing in many human genes. First, after switching on transcription of SAMD4A, a gene with a 134 kb-long first intron, splicing joins the 3 end of exon 1 to successive points within intron 1 well before the acceptor site at exon 2 is made. Second, genome-wide analysis shows that |60% of active genes yield products generated by such intermediate intron splicing. These products are present at ∼15% the levels of primary transcripts, are encoded by conserved sequences similar to those found at canonical acceptors, and marked by distinctive structural and epigenetic features. Finally, using targeted genome editing, we demonstrate that inhibiting the formation of these splicing intermediates affects efficient exon-exon splicing. These findings greatly expand the functional and regulatory complexity of the human transcriptome.
Dear fly people: I have been trying to find some references about the cases in Drosophila in which one genes coding sequence (exon) resides in another genes intron region. I heard of examples, but would like to have a few papers to look at. Could someone give me a quick hand? Thanks a lot ...
All ESTs in GenBank on the date of the track data freeze for the given organism are used - none are discarded. When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site.. ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism.. The maximum intron length allowed by Blat is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously (i.e. an intron has been spliced out), it is also a candidate for the Spliced EST track, provided it meets various quality ...
All ESTs in GenBank on the date of the track data freeze for the given organism are used - none are discarded. When two ESTs have identical sequences, both are retained because this can be significant corroboration of a splice site.. ESTs are aligned against the genome using the Blat program. When a single EST aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within a selected percentage of the best are kept. Alignments must also have a minimum base identity to be kept. For more information on the selection criteria specific to each organism, consult the description page accompanying the EST track for that organism.. The maximum intron length allowed by Blat is 500,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. If an EST aligns non-contiguously (i.e. an intron has been spliced out), it is also a candidate for the Spliced EST track, provided it meets various quality ...
To test for conservation, researchers need to find matching stretches in the two species. This is relatively easy for stretches that code for proteins, where scientists long ago learned the meaning of the sequence. For noncoding regions, however, the comparison is often ambiguous. Even within a gene, stretches of DNA that code for pieces of the target protein are usually interspersed with much larger noncoding stretches, called introns, that are removed from the RNA working copy of the DNA before the protein is made.. Previously, researchers assumed that mutations in the middle of introns do not affect the final protein, so they simply accumulate. In the new study, however, the researchers found signs that evolution rejects some types of mutations even in these regions of the genome. Although the selection is weak, introns are not neutral, in their effect on survival, says CSHLs Michael Zhang, who headed the research team.. To look for selection, co-researcher Chaolin Zhang looked in the ...
Gene can be much larger than unit that codes for protein(as u can conclude)Introns vary while exones are quite conserved(cause selection removes carriers of severe mutations in exones). Very long genes are the result of very long introns! In some techiniques you compare lengths of of alleles. That could be a sign of genetical relation. Could, but not definitely cause same lengh doesnt mean same nucleotide order. But if u compare more polymorphic regions and get covering in size between 2 individuals, the possibility that they are related is higher(again same size doesnt mean same nucleotide order ...
Introns interrupt almost every eukaryotic protein-coding gene, yet how the splicing apparatus interprets the genome during messenger RNA (mRNA) synthesis is poorly understood. We designed microarrays to distinguish spliced from unspliced RNA for each intron-containing yeast gene and measured genomewide effects on splicing caused by loss of 18 different mRNA processing factors. After accommodating changes in transcription and decay by using gene-specific indexes, functional relationships between mRNA processing factors can be identified through their common effects on spliced and unspliced RNA. Groups of genes with different dependencies on mRNA processing factors are also apparent. Quantitative polymerase chain reactions confirm the array-based finding that Prp17p and Prp18p are not dispensable for removal of introns with short branchpoint-to-3′ splice site distances. ...
Supplementary Materials [Supplemental material] jbacter_187_15_5437__index. II introns are genetic retroelements capable of self-splicing and mobility that are common in prokaryotes. Originally discovered in organelles of Read More ...
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A genomic DNA encoding an E8-like gene (CmE8, accession number AB071820) was isolated from melon and its nucleotide sequence was determined. The CmE8 consisted of three exons and two introns. The number and size of the exons and the location of introns were identical to those in tomato E8 gene. The deduced amino acid sequence of CmE8 consisted of 367 amino acids, and it was similar to those of 2-o ...
A catalogue of known hemiascomycetous yeast splicing signals was then used as bait to screen the batch of selected coding sequences, and to validate or not the presence of an intron ...
Intron je nukleotidna sekvenca unutar gena koja se uklanja putem RNK splajsovanja tokom formiranja finalnog RNK proizvoda.[1][2] Termin intron se odnosi na DNK sekvencu unutar gena, i odgovarajuću sekvencu RNK transkripta.[3] Sekvence koje se spajaju u finalnu maturiranu RNK nakon RNK splajsovanja su eksoni. Introni su prisutni u genima većine organizama i mnogim virusima. Oni se mogu naći u širokom nizu gena, uključujući one koji kodiraju proteine, ribozomsku RNK (rRNK), i transportnu RNK (tRNK). Tokom formirana proteina iz gena koji sadrže introne, dolazi do RNK splajsovanja nakon transkripcije i pre translacije. Reč intron je izvedena iz termina intrageni region, i.e. region unutar gena. ...
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英創科技股份有限公司(Intron Scientific Co., Ltd.)成立於1995年7月,『INTRON』原意是人類遺傳的主要組成DNA中一個重要成分代表『英創科技』的核心精神在於建立以「人」為公司最重要資產的核心價值觀,包括員工、顧客供應商以及投資人。實收資本額三千五百萬元整。 將最新
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very
TY - JOUR. T1 - A functional role for some Fugu introns larger than the typical short ones. T2 - The example of the gene coding for ribosomal protein S7 and snoRNA U17. AU - Cecconi, Francesco. AU - Crosio, Claudia. AU - Mariottini, Paolo. AU - Cesareni, Gianni. AU - Giorgi, Marcello. AU - Brenner, Sydney. AU - Amaldi, Francesco. PY - 1996. Y1 - 1996. N2 - The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. We have analyzed the Fugu gene for ribosomal protein S7 (formerly S8, see Note), whose Xenopus homolog contains in its introns the coding sequences for the small nucleolar RNA U17. Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. The total length of the Fugu S7 gene is 3930 bp, compared with 12691 bp for Xenopus. This length difference is uniquely due to smaller introns. Although short, the six introns are longer than the ~100 bp size of most ...
Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (PF00078) followed by an RNA-binding maturase domain (PF08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029 ...
Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life. We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three ...
Two types of spliceosomes catalyze splicing of pre-mRNAs. The major U2-type spliceosome is found in all eukaryotes and removes U2-type introns, which represent more than 99% of pre-mRNA introns. The minor U12-type spliceosome is found in some eukaryotes and removes U12-type introns, which are rare and have distinct splice consensus signals. The U12-type spliceosome consists of several small nuclear RNAs and associated proteins. This gene encodes a 65K protein that is a component of the U12-type spliceosome. This protein contains two RNA recognition motifs (RRMs), suggesting that it may contact one of the small nuclear RNAs of the minor spliceosome. [provided by RefSeq, Jul 2008 ...
The fission yeast genome, which contains numerous short introns, is an apt model for studies on fungal splicing mechanisms and splicing by intron definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA-processing factor, SpPrp18. Our mutational and biophysical analyses of the C-terminal alpha-helical bundle reveal critical roles for the conserved region as well as helix five. We generate a novel conditional missense mutant, spprp18-5. To assess the role of SpPrp18, we performed global splicing analyses on cells depleted of prp18(+) and the conditional spprp18-5 mutant, which show widespread but intron-specific defects. In the absence of functional SpPrp18, primer extension analyses on a tfIId(+) intron 1-containing minitranscript show accumulated pre-mRNA, whereas the lariat intron-exon 2 splicing intermediate was undetectable. These phenotypes also occurred in cells lacking both SpPrp18 and SpDbr1 (lariat debranching enzyme), a genetic ...
BackgroundThe genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution.Methodology/Principal FindingsHere we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the
TY - JOUR. T1 - An alternative route for the folding of large RNAs. T2 - Apparent two-state folding by a group II intron ribozyme. AU - Su, Linhui Julie. AU - Brenowitz, Michael. AU - Pyle, Anna Marie. N1 - Funding Information: The authors thank Tobin Sosnick, Art Palmer, Eric Gouaux, and Andrew Miranker for insightful advice and suggestions, Peter Moore for suggesting hydrodynamic techniques for studying group II introns, Alex de Lencastre and Christina Waldsich for helpful discussions on the manuscript, and Rich Olson for advice on analytical ultracentrifugation. Funding for the Jasco J810 Spectropolarimeter was obtained from NIH grant GM34509 to Koji Nakanishi. Funding for the Beckman XL-I centrifuges were obtained from NIH shared instrumentation grant S10 RR12848 to Columbia University and GM54160 to Donald Engelman (Yale University). We acknowledge funding from NIH to L.J.S. (Biophysics Training Grant T32 GM08281), M.B. (GM52348), and A.M.P. (RO1 GM50313). A.M.P. is an Investigator of the ...
DNA is made up of different units called nucleotides. There are a variety of four different nucleotides that make up the polymer that is DNA[1]. DNA consists of two different regions, one being exons and the other introns. The regions of exons in the DNA consist of fewer nucleotides than the regions of introns and are the regions that code for proteins[2]. It is also now thought that enhancer sequences for regulation of gene transcription is not just found in introns but also exons.[3]. Exons are the coding regions of a gene and are separated by regions of introns; they are copied during transcription (along with introns) to produce pre-mRNA[4] ...
TY - JOUR. T1 - Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene. AU - Fukumura, Kazuhiro. AU - Kato, Ayako. AU - Jin, Yui. AU - Ideue, Takashi. AU - Hirose, Tetsuro. AU - Kataoka, Naoyuki. AU - Fujiwara, Toshinobu. AU - Sakamoto, Hiroshi. AU - Inoue, Kunio. PY - 2007/8/1. Y1 - 2007/8/1. N2 - Fox-1 is a regulator of tissue-specific splicing, via binding to the element (U)GCAUG in mRNA precursors, in muscles and neuronal cells. Fox-1 can regulate splicing positively or negatively, most likely depending on where it binds relative to the regulated exon. In cases where the (U)GCAUG element lies in an intron upstream of the alternative exon, Fox-1 protein functions as a splicing repressor to induce exon skipping. Here we report the mechanism of exon skipping regulated by Fox-1, using the hF1γ gene as a model system. We found that Fox-1 induces exon 9 skipping by repressing splicing of the downstream intron 9 ...
Author: Britanova, O. et al.; Genre: Journal Article; Published in Print: 2002-07; Keywords: cortex; transcription factor; subtraction; Sey; reeler; mutant|br/|; Title: The mouse Laf4 gene: Exon/intron organization, cDNA sequence, alternative splicing, and expression during central nervous system development
The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this paper, we define a set of features, called the simple Z (SZ) features, which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that SZ features, while fewer in numbers ~three in total!, can preserve the high recognition rate of the original nine Z-curve features. Since the size of SZ features is one-third of the Z-curve features, the dimensionality of the feature space is much smaller, and better recognition efficiency is achieved. If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of length ,140 bp can be obtained ...
In contrast to bacteria which have no introns, eukaryotes (cells with a nucleus) have introns which are intervening sequences within genes which get spliced out when genes are transcribed and are not expressed in the protein. In contrast, exons are the sequences within a gene which do get expressed and translated into protein. Intergenic DNA, as the name suggests, is DNA between genes which does not code for proteins. Hope this helps gabriel vargas md/phd References Genes VII by Benjamin Lewin ...
This is a pretty good article on the origin of the spliceosome from self-splicing introns: Vosseberg J, Snel B. Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery. Biol Direct. 2017 Dec 1;12(1):30. DOI:10.1186/s13062-017-0201-6 There are many interesting references given in that article also, for example on spliceosomal diversity. There are simple protozoan parasites known with as few as 27 introns in their entire genomes, and highly s...
Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms ...
import pysam from collections import Counter from CGAT import GTF, IOTools def calculateSplicingIndex(bamfile, gtffile, outfile): bamfile = pysam.AlignmentFile(bamfile) counts = Counter() for transcript in GTF.transcript_iterator( GTF.iterator(IOTools.openFile(gtffile))): introns = GTF.toIntronIntervals(transcript) for intron in introns: reads = bamfile.fetch( reference=transcript[0].contig, start=intron[0], end=intron[1]) for read in reads: if N in read.cigarstring: blocks = read.get_blocks() starts, ends = zip(*blocks) if intron[0] in ends and intron[1] in starts: counts[Exon_Exon] += 1 else: counts[spliced_uncounted] += 1 elif (read.reference_start ,= intron[0] - 3 and read.reference_end ,= intron[0] + 3): if transcript[0].strand == +: counts[Exon_Intron] += 1 else: counts[Intron_Exon] += 1 elif (read.reference_start ,= intron[1] - 3 and read.reference_end ,= intron[1] + 3): if transcript[0].strand == +: counts[Intron_Exon] += 1 else: counts[Exon_Intron] += 1 else: ...
By Michael Marshall. Patches of seemingly meaningless DNA dotted throughout the genome might actually have a function: helping cells to survive starvation.. Two studies published in Nature on 16 January suggest that these stretches of non-coding DNA called introns help to control the rate at which cells grow, conserving energy when food becomes scarce.. Genes carry the information needed to make proteins. But many genes contain introns: sequences of non-coding DNA, the vast majority of which dont appear to do anything.. Some researchers suspected introns did more than meets the eye.. In one of the latest studies1, Sherif Abou Elela, a microbiologist at the University of Sherbrooke in Quebec, Canada, and his colleagues examined bakers yeast (Saccharomyces cerevisiae), whose DNA has 295 introns. They spent ten years meticulously creating hundreds of yeast strains, each missing just one of its introns.. Continue reading by clicking the name of the source below.. ...
Responsibilities: He conducted PCR and DNA sequencing experiments to gather DNA sequence data from the b-fibrinogen gene for selected avian orders. DNA sequence was used in subsequent phylogenetic analyses. Developed three additional novel intron sequences from other nuclear genes for use in further phylogenetic analyses of avian species. Evaluated the statistical comparison of the base composition, distribution of substitutions, transition / transversion ratio, degree of homoplasy, and variation in substitution rates among the introns. He additionally explored DNA sequence patterns in introns of nuclear genes for the purpose of locating possible gene promoter and transcription factor binding sites and their possible link to gene expression ...
p,,strong,Frameshift introns,/strong, are the length of 1, 2, 4, or 5 basepairs. They are introduced by the Ensembl ,a href=../../../info/genome/genebuild/index.html,genebuild,/a, in order to fit the cDNA sequence to the genome.,/p,Frameshift introns occur at intron number(s) 16. ...
For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience. Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome sequence. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result
1. In the context of a new mammalian model organism recently sequenced and annotated, gene YFG has 3 introns and 4 exons. Databases show that there are 3 different lengths of cDNA sequences associated with Gene YFG. One of these cDNA sequences has three out of four exons plus additional nucleotide sequence at the 3 end of the cDNA. This part codes for an extra 123 amino acids. Annotated gene UB2, appears immediately downstream of YFG. UB2 has a single exon coding for 123 amino acids matching the cDNA. There is no cDNA in your database encoding for a UB2 gene with these 123 amino acids at the N-terminus ...
To assess whether the discrepancy between the protein and mRNA levels was due to the presence of variant embryonic proinsulin transcripts, we carried out a detailed RT-PCR study during gastrulation, neurulation and early organogenesis (Fig 2). PCR with the P3 and P5 primers showed two amplification products (Fig 2A,B). Cloning and sequencing of these PCR products showed that the larger band corresponded to an alternatively spliced isoform (Pro1B1) of the embryonic proinsulin transcript; it retained intron 1 (717 nt) in the 5′ UTR, but spliced out intron 2 (3,432 nt). Both spliced and intron‐retained embryonic transcripts were polyadenylated, since oligo‐dT was used in the RT reaction. The intron 1 splicing pattern is developmentally regulated; the intron 1‐containing isoform was nearly undetectable during gastrulation (st. 4), and the percentage of intron 1 retention increased throughout neurulation (st. 8-10) and organogenesis (st. 12; Fig 2B,C). No PCR products were detected in the ...
Mitochondrial Mg (super.2+) homeostasis is critical for group II intron splicing in vivo. Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo
Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of nine group II introns in maize chloroplasts. CRS2 functions in the context of splicing complexes that include one of two CRS2-associated factors (CAF1 and CAF2). The CRS2-CAF1 and CRS2-CAF2 complexes are requ …
The mdm2 gene is a target for transcriptional activation by the p53 tumor suppressor gene product. Previous work has revealed that the mouse mdm2 gene contains two promoters: one is located upstream to the gene and is active in the absence of p53, the other resides within the first intron and requires p53 for transcriptional activity. To determine whether this unique promoter activation pattern is biologically important, we investigated the structure and function of the corresponding region of the human mdm2 (hmdm2) gene. We report here that the hmdm2 gene also contains an intronic, p53-dependent promoter. The structural features of this promoter are highly conserved between mouse and man, as opposed to the lack of conservation of the first exon. This promoter is triggered in vivo in the presence of activated wild type p53, leading to the production of novel mRNA species. The intronic hmdm2 promoter contains two tandem p53 binding elements. Deletion analysis suggests that optimal promoter
Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.
RNA Splicing Definition RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns. The process of RNA splicing involves the … Read more. ...
Exon sequences are conserved, but intron sequences vary, Organization of Genetic Material Split Genes, Overlapping Genes and Pseudogenes, Genetics
This sequence change falls in intron 3 of the SPRED1 gene. It does not directly change the encoded amino acid sequence of the SPRED1 protein. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SPRED1-related disease. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, this is a novel intronic change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance ...
I am looking at RNA-seq data, which I have little experience in. I notice that for many genes, there are reliable alignments (i.e. with high mapping quality) to introns. I understand that some of them are due to unannotated transcripts, but in many regions, this does not seem to be the major cause. The intronic read hits do not seem to be purely caused by alignments artifacts, either, because the pattern is tissue specific (though this is not a compelling evidence). Another possible explanation is that this observation is due to noisy transcripts (Pickrell et al, 2010), but this seems to be a big effect: for some long genes, there are far more intronic hits than exonic hits.. I guess those who study RNA-seq data must have noticed the intronic hits for years. What is cause of the large amount of intronic read hits? Is it caused by alignment/library prep artifacts or noisy transcription? Are there papers addressing this? Thanks.. EDIT: my conclusion. I was looking at ERR030882 from Illumina ...
A transcript is the operational unit of a gene. In a genomic context, transcripts consist of one or more exons, with adjoining exons being separated by introns. The exons/introns are transcribed and then the introns spliced out. Transcripts may or may not encode a proteinGene transcripts ...
Once transcription is complete, there are further controls that allow the network of enzymes and genes to control itself. Im not going to list all of them, but one that cannot be left out involves alternative splicing of RNA. This is a process in which the transcribed RNA is edited, usually removing a number of sections called introns, while creating the final mRNA. Which introns are removed, and sometimes where their boundaries are set, determines the sequence of the final mRNA, and thus the character of the protein. Alternative splicing can be affected by enzymes, but also by non-coding RNAs of various types and provenance, including those snipped out of the introns of other genes. A description of some of the ways in which alternative splicing can be regulated may be found in Regulation of Alternative Splicing: More than Just the ABC by Amy E. House and Kristen W. Lynch. It may turn out that the number of data connections that affect protein (enzyme) concentration via regulation of internal ...
This sequence change falls in intron 14 of the PNKP gene. It does not directly change the encoded amino acid sequence of the PNKP protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs776617733, ExAC 0.04%). This variant has not been reported in the literature in individuals with PNKP-related conditions. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance ...
Parameters: -f ,filename, potential splice sites in gff format -g ,filename, genome file in fasta format -c ,integer, defines the number of potential splice site every potential splice site itself is compared with -t ,float, has to be between 0 and 1 and defines how much the average coverage may differ -m ,integer, defines how many bases around the splice site should be checked -d enables debugging output -i ,integer, maximum length an Intron can be, default 500000 (human genome ...
Read Variants in an Hdac9 intronic enhancer plasmid impact Twist1 expression in vitro, Mammalian Genome on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Loren I. Petrich writes: , , This does not look like the result of spotaneous generation, ,unless one allows for extreme improbabilities, so it is presumed that ,there has been a lot of evolution behind it, evolution that may have ,left some vestiges, in the fashion of the numerous vestigial features ,generated by later evolution (I wonder if anyone has compiled a ,reasonably comprehensive list). Interesting request. How many molecular fossils can you name? Heres a start: rRNA performs catalytic functions in ribosomes (several papers in Science in the last few weeks) tRNA CCA adding enzyme is the first telomerase (Nancy Maizels and Alan Weiner in PNAS a few years ago) self-splicing introns and the role of snRNAs in other intron splicing NTPs as energy-storage media other nucleoside-based cofactors (NAD, CoA, etc.) mRNA , , A system where there are two kinds of nucleic acids and where ,RNA was the original molecule, with DNA a specialization for long-term ,information storage. This is from ...
originalDATA1ofFigS3C.tif : Full-length western blotting images used in Fig S3C (HEK293 cells). originalDATA2ofFigS3C.tif : Full-length western blotting images used in Fig S3C (U2OS cells). originalDATA3ofFigS7B.tif : Full-length western blotting images used in Fig S7B.
Genes in eukaryotic organisms are frequently interrupted by non-coding segments called introns. Before the protein can be produced, the entire length of each gene including the introns, is transcribed to produce precursor messenger RNA (pre-mRNA).
Im working on a chapter about pervasive transcription and how it relates to the junk DNA debate. I found a short review in Nature from 2002 so I decided to see how much progress weve made in the past 15 years.. Most of our genome is transcribed at some time or another in some tissue. Thats a fact weve known about since the late 1960s (King and Jukes, 1969). We didnt know it back then, but it turns out that a lot of that transcription is introns. In fact, the observation of abundant transcription led to the discovery of introns. We have about 20,000 protein-coding genes and the average gene is 37.2 kb in length. Thus, the total amount of the genome devoted to these genes is about 23%. Thats the amount thats transcribed to produce primary transcripts and mRNA. There are about 5000 noncoding genes that contribute another 2% so genes occupy about 25% of our genome ...
Im working on a chapter about pervasive transcription and how it relates to the junk DNA debate. I found a short review in Nature from 2002 so I decided to see how much progress weve made in the past 15 years.. Most of our genome is transcribed at some time or another in some tissue. Thats a fact weve known about since the late 1960s (King and Jukes, 1969). We didnt know it back then, but it turns out that a lot of that transcription is introns. In fact, the observation of abundant transcription led to the discovery of introns. We have about 20,000 protein-coding genes and the average gene is 37.2 kb in length. Thus, the total amount of the genome devoted to these genes is about 23%. Thats the amount thats transcribed to produce primary transcripts and mRNA. There are about 5000 noncoding genes that contribute another 2% so genes occupy about 25% of our genome ...
Alternative splicing was the first phenomenon scientists discovered that made them realize that genomic complexity cannot be judged by the number of protein-coding genes. During alternative splicing, which occurs after transcription and before translation, introns are removed and exons are spliced together to make an mRNA molecule. However, the exons are not necessarily all spliced back together in the same way. Thus, a single gene, or transcription unit, can code for multiple proteins or other gene products, depending on how the exons are spliced back together. In fact, scientists have estimated that there may be as many as 500,000 or more different human proteins, all coded by a mere 20,000 protein-coding genes. ...
Turunen, J. J.; Will, C. L.; Grote, M.; Luehrmann, R.; Frilander, M. J.: The U11-48K protein contacts the 5 splice site of U12-Type introns and the U11-59K protein. Molecular and Cellular Biology 28 (10), pp. 3548 - 3560 (2008 ...
There are many classic examples of evidence that support evolution, such as endogenous retroviruses or transitional fossils, but I would like to focus on another piece of evidence that I think is just as powerful and hop…
Ive been sewing since I was 4. Barbie doll clothes made way for maxi skirts, to mini skirts, to 3 piece suits. Upholstered pieces followed, and then I learned how to quilt ...
The classical gene codes for a protein; the genetic code is transcribed into a strand of RNA by RNA polymerase. This RNA, known as pre-messenger RNA, undergoes splicing where the introns are removed. Once completed, the messenger RNA is transported to the ribosomes in the cytoplasm for translation into protein ...
There are five tracks in this figure. The x-axis at the bottom shows the sequence coordinates on this chromosome in the human genome. The top track shows the organization of genes that cover this region. In this case we can see from the arrowhead at the left end that BRCA1 is encoded on the reverse strand of the DNA, running right to left.. The small blue blocks represent the exons in this gene, separated by the much larger introns. The track below this shows the location of sequence repeats, with the colors representing different types. The genome is packed full of these so-called junk sequences, the functions of which are still unclear. Notice that the repeats account for most, but not all, of the intron sequences. The two large tracks with the peaks and valleys display how well the human sequence is conserved in the genomes of mouse and rat, respectively. The similarity plot is truncated at 50% so any peaks shown indicate strong similarity. These two plots look broadly the same, indicating ...
The G of the donor site is joined covalently to the A of the branch site. This structure is excised at the 3 end of the acceptor site, and the ends of the two adjacent exon equivalents are joined. ...
View Notes - Lecture.14.Fall.2013 from BIOLOGY 115 at San Jose State. in eukaryotes are colinear within exons, but are interrupted by noncoding sequences Introns vary in length, and are longer, on
Effects within introns[edit]. Microsatellites within introns also influence phenotype, through means that are not currently ... 1995). "The barley Hooded mutation caused by a duplication in a homeobox gene intron". Nature. 374 (6524): 727-730. Bibcode: ... For example, a GAA triplet expansion in the first intron of the X25 gene appears to interfere with transcription, and causes ... If searching for microsatellite markers in specific regions of a genome, for example within a particular intron, primers can be ...
Within introns, a donor site (5' end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end ... Two models have been proposed: the intron late and intron early models (see intron evolution). ... Introns[edit]. The word intron is derived from the terms intragenic region,[1] and intracistron,[2] that is, a segment of DNA ... There are three kinds of self-splicing introns, Group I, Group II and Group III. Group I and II introns perform splicing ...
... s, Introns and DNA damage[edit]. Introns are non-coding regions within genes that are transcribed along with the coding ... Introns reduce R-loop formation and DNA damage in highly expressed yeast genes.[22] Genome-wide analysis showed that intron- ... R-loop mapping is a laboratory technique used to distinguish introns from exons in double-stranded DNA.[8] These R-loops are ... An illustration showing how a DNA-mRNA hybrid forms R-Loops in the regions where introns have been removed through splicing ...
Notches indicate introns. Chloroplasts have their own DNA, often abbreviated as cpDNA. It is also known as the plastome when ... Introns are common in chloroplast DNA molecules, while they are rare in prokaryotic DNA molecules (plant mitochondrial DNAs ... commonly have introns, but not human mtDNA). Among land plants, the contents of the chloroplast genome are fairly similar-they ...
Notches indicate introns. With few exceptions, most chloroplasts have their entire chloroplast genome combined into a single ... Unlike prokaryotic DNA molecules, chloroplast DNA molecules contain introns (plant mitochondrial DNAs do too, but not human ...
When testing the effect of unc-5::intron::unc-5 transgene on a mislocalization defect in UNC-5 mutant animals at 25 °C a ...
... contains 18 introns. There are 2 non overlapping alternative last exons. The transcripts appear to differ by truncation of ... MCM6 produces, by alternative splicing, 3 different transcripts, all with introns, putatively encoding 3 different protein ... located in two of the MCM6 introns, approximately 14 kb (-13910) and 22 kb (-22018) upstream of LCT. The (-13910) region, in ...
Bürglin TR, Barnes TM (1992). "Introns in sequence tags". Nature. 357 (6377): 367-8. Bibcode:1992Natur.357..367B. doi:10.1038/ ...
The NFR5 gene lacks introns. First the cell membrane is depolarized and the root hairs start to swell and cell division stops. ...
This gene contains no introns. A pseudogene of this gene is present on chromosome 14. GRCh38: Ensembl release 89: ...
"A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility". Cell. 83 (4): 529-38. doi: ... July 2001). "Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate". EMBO J. 20 (14 ... Open reading frames encoding homing endonucleases have been found in introns, inteins, and in freestanding form between genes, ... Lambowitz AM, Belfort M (1993). "Introns as mobile genetic elements". Annu Rev Biochem. 62: 587-622. doi:10.1146/annurev.bi. ...
Mobile introns are frequently members of either the group I or group II families of self-splicing introns. Introns are removed ... These introns can be regarded as examples of selfish DNA. Some mobile introns encode homing endonucleases, enzymes that ... Nuclear pre-mRNA introns and spliceosome-associated snRNAs show similar structural features to self-splicing group II introns. ... In addition, the splicing pathway of nuclear pre-mRNA introns and group II introns shares a similar reaction pathway. These ...
The gene has no introns; the single exon is approximately 1.5kb in size. FOX transcription factors are expressed during ...
He was awarded the 1993 Nobel Prize in Physiology or Medicine with Phillip Allen Sharp for the discovery of introns in ...
... chloroplast DNA molecules contain introns (plant mitochondrial DNAs do too, but not human mtDNAs).[79] ...
The introns were not placed randomly; they fell in the center of the region of amino acid sequence homology in strikingly ... Altruda F, Poli V, Restagno G, Silengo L (1988). "Structure of the human hemopexin gene and evidence for intron-mediated ... 1988) concluded that the gene evolved through intron-mediated duplications of a primordial sequence to a 5-exon cluster. Cai ... "Structure of the human hemopexin gene and evidence for intron-mediated evolution". Journal of Molecular Evolution. 27 (2): 102- ...
Zimmerly, Steven (2005). "Mobile introns and retroelements in bacteria". In Mullany, Peter (ed.). The Dynamic Bacterial Genome ...
The number of foreign DNA elements (exon and introns) inserted into the constitutive exons and introns of a given fragment ... Errors in tau splicing can occur in both exons and introns and, depending on the error, result in changes to protein structure ... Minigenes were used to determine that a point mutation within an intron splice enhancer (ISE) embedded in IVS3 was to blame for ... Once a suitable genomic fragment is chosen (Step 1), the exons and introns of the fragment can be inserted and amplified, along ...
The gene contains 20 distinct introns. Transcription produces 15 different mRNAs, 10 alternatively spliced variants and 5 ... splicing versus retention of 3 introns. The San Diego Super Computer's Statistical Analysis of Protein (SAPS) program ...
This gene does not contain introns. ANP32A, ANP32B, ANP32D, ANP32E GRCh38: Ensembl release 89: ENSG00000248546 - Ensembl, May ...
"A difficult phase for introns-early. Molecular evolution". Current Biology. 6 (5): 533-36. doi:10.1016/S0960-9822(02)00535-3. ...
RNAseq introns :: single sample supports all introns ERS025083, ERS025084 [ECO:0000348] ##Evidence-Data-END## Kazal-type serine ...
... contains 6 exons and 5 introns. There are two paralogs for this gene, SLC46A1 and SLC46A2, and orthologs as distant as ... Lengths shown do not include introns. 3 isoforms have been reported for SLC46A3. Isoform a is MANE select and most abundant. ...
Indeed, the intron regions of a gene can be considerably longer than the exon regions. Once spliced together, the exons form a ... Introns are extremely rare in prokaryotes and therefore do not play a significant role in prokaryotic gene regulation. This ... A key feature of the structure of eukaryotic genes is that their transcripts are typically subdivided into exon and intron ... Exon regions are retained in the final mature mRNA molecule, while intron regions are spliced out (excised) during post- ...
Two models have been proposed: the intron late and intron early models (see intron evolution). Spliceosomal splicing and self- ... end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end of the intron) are required for ... The consensus sequence for an intron (in IUPAC nucleic acid notation) is: G-G-[cut]-G-U-R-A-G-U (donor site) ... intron ... There are three kinds of self-splicing introns, Group I, Group II and Group III. Group I and II introns perform splicing ...
RNAseq introns :: mixed/partial sample support ERS025084, ERS025088 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes- ...
Several introns contain Alu repetitive sequences. A TATA-like sequence (TTATAAAA) and a CAAT-like sequence (GTCATCAT) are ...
Clancy, Suzanne (2008). "RNA Splicing: Introns, Exons and Spliceosome". Nature Education. 1 (1). Retrieved 31 March 2011. ... it sometimes contains intervening or interrupting sequences named introns. mRNA splicing helps to remove these sequences, ...
Introns in the T-Even Bacteriophages. PhD thesis. University of Colorado at Boulder. (Chapter 3 provides overview of various T4 ... The T4 genome bears eukaryote-like intron sequences. The Shine-Dalgarno sequence GAGG dominates in virus T4 early genes, ...
Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron. Introns of the same ... Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. ... 5' cap or3' poly A flags show completeness of the transcript . CORO6 contains 21 distinct gt-ag introns. Transcription produces ...
Introns is a remix album by the American rock band LCD Soundsystem, released in March 2006 through DFA as a digital download. ...
... and possibly to spliceosomal introns. Nuclear pre-mRNA introns (spliceosomal introns) are characterized by specific intron ... Intron transfer has been hypothesized to result in intron gain when a paralog or pseudogene gains an intron and then transfers ... This intron-containing mRNA is then reverse transcribed and the resulting intron-containing cDNA may then cause intron gain via ... In intron transposition, the most commonly purported intron gain mechanism, a spliced intron is thought to reverse splice into ...
It would help enormously if I could tell where the introns would be. (Trying to PCR a 50kb+ intron might be a tad difficult ... Introns and Exons again.... Dr. N.A. Affara naffara at crc.ac.uk Wed Oct 7 10:19:36 EST 1992 *Previous message: Automated ... I have had several replies about max length of introns (200kb?) but not much about average length of introns and exons. Thanks ... Is there any way of finding out where the intron/exon (exon-exon) boundaries are in a cDNA sequence? I am trying to design PCR ...
An intron is a portion of a gene that does not code for amino acids. In the cells of plants and animals, most gene sequences ... And these introns get removed from the RNA molecule to leave a string of exons attached to each other so that the appropriate ... Introns are very large chunks of RNA within a messenger RNA molecule that interfere with the code of the exons. ... while the parts of the gene sequence that are not expressed in the protein are called introns, because they come in between the ...
As controls, 12 oligos were chosen for rrn16, rbcL, psbA, the ndhB intron, the rpl16 intron, and the petD intron, none of which ... The only plastid group IIA intron not identified in either type of analysis as a MatK target was the second intron in the clpP ... Further attempts to detect clpP-intron 2 in slot-blot assays were negative (Fig. S2). The clpP intron 2 is a structural ... 3B and Table S1). Seven of the eight most strongly enriched RNAs carry introns from the structurally defined group IIA intron ...
So i am interested in all information about number of introns in A. thaliana genes and the smallest/biggest introns/exons. The ... Number and size of Arabidopsis introns. Frank Hartung hartung at ipk-gatersleben.de Tue Dec 8 12:37:48 EST 1998 *Previous ... Dear Netters, I am working with different new genes of A. thaliana which are containing a relatively big number of introns ( ...
5.0100). Homozygous diploid intron-minus glc7Δi/glc7Δi strains were created by mating a and α intron-minus strains and diploids ... All intron-minus strains were constructed using PCR-based gene replacement (Wach 1996). Intron-minus glc7Δi strains were ... Intron knockouts produce less RNA than wild-type genes:. The results from our genomic studies suggest that introns serve to ... Intron position and length correlate with gene expression:. The question arises, How do introns increase RNA and protein output ...
PEG-Intron): learn about side effects, dosage, special precautions, and more on MedlinePlus ... Peginterferon Alfa-2b (PEG-Intron). pronounced as (peg in ter feer on) ...
BACK to Hemiascomycetous Yeast Spliceosomal Introns 1. Search for S. cerevisiae-like introns. S. cerevisiae introns. (MIPS, ... and to validate or not the presence of an intron. Yeast species. Number of genes. with introns. 5 motif. Branch motif. 3 ... b Compilation of intron sequences available at NCBI (release of June 2001). Last modified: Tue Feb 10 11:14:44 CET 2004 ... 252 genes / 260 introns. <<====>>. S. cerevisiae homologues. 9764 coding sequences,. either full length or partial. ...
Intron. (Redirected from Introns). For the interferon-based drug used in viral and cancer treatments, see Intron A. For the ... Intron transfer has been hypothesized to result in intron gain when a paralog or pseudogene gains an intron and then transfers ... See also: Group I catalytic intron and Group II intron. Group I and group II introns are found in genes encoding proteins ( ... Spliceosomal intronsEdit. See also: RNA splicing § Spliceosomal. Nuclear pre-mRNA introns (spliceosomal introns) are ...
In contrast to bacteria which have no introns, eukaryotes (cells with a nucleus) have introns which are intervening sequences ... Re: What is intergenic DNA compared to introns and exons?. Date: Fri May 5 16:40:29 2000. Posted By: Gabriel Vargas M.D.,Ph.D ...
... elegans the difference in intron length is only twofold. In contrast, the density of introns in a gene does not strongly depend ... Selection for short introns in highly expressed genes.. Castillo-Davis CI1, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. ... Using data on the expression of genes that encode proteins in Caenorhabditis elegans and Homo sapiens, we show that introns in ... This difference is greater in humans, such that introns are, on average, 14 times shorter in highly expressed genes than in ...
While nearly all TEs within introns appear harmless, some de novo intronic TE insertions do disrupt gene transcription and ... are major constituents of mammalian genomes and are found within introns of most genes. ... Introns Is the Subject Area "Introns" applicable to this article? Yes. No. ...
Arabidopsis intron mutants provide and will continue to provide a valuable source of information on in vivo plant intron ... Arabidopsis intron mutations and pre-mRNA splicing.. Brown JW1.. Author information. 1. Department of Cell and Molecular ... This splicing behaviour is in agreement with detailed splicing analyses of test plant introns. However, some of the Arabidopsis ... Analysis of the Arabidopsis intron mutations exhibiting complex splicing patterns will help to address fundamental questions in ...
Peg-Intron (peginterferon alfa-2b): For the treatment of chronic hepatitis C. New approved drug details including side effects ... Peg-Intron is a longer-acting formulation of Schering-Ploughs Intron A, which is a recombinant version of a naturally ... In contrast to Intron A, which is administered three times weekly, Peg-Intron is administered subcutaneously once a week. This ... The trial compared Peg-Intron (0.5, 1.0 or 1.5 mcg/kg) administered subcutaneously once weekly to Schering-Ploughs Intron A ( ...
Intron gain accounts for the vast majority of extant introns...".. Eirik W. Lundblad et al., "Twelve Group I Introns in the ... Introns first?. Scott William Roy and David Penny, "Large-scale intron conservation and order-of-magnitude variation in intron ... Convincing support for "introns-late" without accounting for the origin of introns.. Ancient Protozoan [has an intron] by ... Introns Early? Introns Late?. Darwinists responded to the discovery of introns by guessing that they arose either early or late ...
... it soon became apparent that introns contained many different codes needed for proper gene function.2-4 In some cases, introns ... Introns are mediators of cell response to starvation. Nature. doi.org/10.1038/s41586-018-0859-7.. Dr. Jeffrey Tomkins is ... But most importantly, introns were found to play important roles in the alternative splicing of exons so that a single gene ... At first, introns seemed to contain useless information that did not contribute to the final protein product created from an ...
A) Exon/intron structures of cox1 and cob, with exons depicted as black boxes connected by gray lines (introns). Introns known ... In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron- ... C) SNP density as a function of distance from the nearest intron-exon boundary for introns in intron-containing mitochondrial ( ... pombe reference genome encodes two introns in cox1 and a single intron in cob. Importantly, the group II cob intron alone is ...
Heterologous intron sequences from a Cd4 locus were also functional in directing hCD2 expression in CD8+ T cells. Intron ... 2000) Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing. Plant Physiol 122:535 ... 5) reported that several different introns enhance expression of the same gene in maize. During IME, the intron increases mRNA ... 1988) Comparison of intron-dependent and intron-independent gene expression. Mol Cell Biol 8:4395-4405. ...
Intron je nukleotidna sekvenca unutar gena koja se uklanja putem RNK splajsovanja tokom formiranja finalnog RNK proizvoda.[1][2 ... Reč intron je izvedena iz termina intrageni region, i.e. region unutar gena. ... Termin intron se odnosi na DNK sekvencu unutar gena, i odgovarajuću sekvencu RNK transkripta.[3] Sekvence koje se spajaju u ... Преузето из „https://sr.wikipedia.org/w/index.php?title=Intron&oldid=21005869" ...
... (intronic numbering for coding DNA Reference ...
... of introns varies considerably between related species. There are four or five different kinds of intron. Some introns ... A spliceosome removes introns from a transcribed pre-mRNA segment (top). This is called splicing. After the introns have been ... There are many unanswered questions about introns. It is unclear whether introns serve some specific function, or whether they ... The term intron was introduced by American biochemist Walter Gilbert.[4] Biological meaning[change , change source]. ...
Peginterferon (PEG-INTRON, Schering Corporation, Kenilworth, NJ) is a new formulation of interferon recently approved for the ...
... The exon/intron organisation of homologous nuclear genes was compared in several yeast species ... Intron sliding or hot spot of intron insertions?. *The YJL166w case Δ = 2 nt *The YDR367w case Δ = 3 nt *The YGR001c case Δ = 3 ... Intron sliding is defined as the relocation of a pre-existing intron over short distances in the course of gene evolution [ ... Intron position was defined at the nucleotide level making it possible to determine whether the intron is at an identical ...
The GC-effect results in a higher GC content in minimal introns than their flanking exons as opposed to larger introns (≥125 nt ... Conclusions We validated the unique mutation dynamics of minimal introns in keeping their near-optimal size and GC content, and ... Principal Findings We not only confirmed that minimal introns in human populations are selected but also found two major ... effects in minimal intron evolution: (i) Size-effect: minimal introns longer than an optimal size (87 nt) tend to have a higher ...
I dont know why they think that the 1st intron comes before the 1st exon. Everything I have seen shows it the other way around ... I dont know why they think that the 1st intron comes before the 1st exon. Everything I have seen shows it the other way around ... Introns and Exons. Discussion in Step I started by i61164, Feb 27, 2007. ... 3---start codon---(5 untranslated region)---1st intron---1st exon---etc.---5. ...
19, 2018 /PRNewswire/ -- Roivant Sciences and iNtRON Biotechnology today announced that they have entered into a global ... iNtRON Biotechnology, Inc.. Tony Jung. Email. [email protected]intron.co.kr. Roivant Sciences, Inc.. Paul Davis. Email: [email protected] ... About iNtRON Bio. iNtRON Bio is a biotechnology company in Korea focused on the development of bacteriophage/endolysin-based ... For more information, please visit www.intron.co.kr.. About Roivant Sciences Roivant aims to improve health by rapidly ...
However, expression-controlling introns can be identified computationally in species with relatively small introns, based on ... However, expression-controlling introns can be identified computationally in species with relatively small introns, based on ... The genes regulated by introns are often expressed in most tissues and are among the most highly expressed in the genome. The ... However, introns may be particularly useful in practical applications such as gene therapy because they strongly activate ...
En ce qui concerne les g nes un de mes professeurs ma affirm que des introns pouvaient tre pr sent dans un ARNm mature. ... Re : intron vs exon: salut. il y a des prot ines ou des ARN qui sont obtenus a partir des introns. Mais lepissage alternatif ... intron vs exon: Bonjour aux utilisateurs.. En ce qui concerne les g nes un de mes professeurs ma affirm que des introns ... Re : intron vs exon: salut. dans le cadre de l pissage alternatif on peut conserver certains introns.. Dautres part certains ...
Intron A) in Daviss Drug Guide including dosage, side effects, interactions, nursing implications, mechanism of action, half ...
  • must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger - which I suggest we call introns (for intragenic regions) - alternating with regions which will be expressed - exons. (wikipedia.org)
  • Nuclear pre-mRNA introns (spliceosomal introns) are characterized by specific intron sequences located at the boundaries between introns and exons. (wikipedia.org)
  • Nuclear pre-mRNA introns are often much longer than their surrounding exons. (wikipedia.org)
  • Introns and Exons again. (bio.net)
  • but not much about average length of introns and exons. (bio.net)
  • The parts of the gene sequence that are expressed in the protein are called exons, because they are expressed, while the parts of the gene sequence that are not expressed in the protein are called introns, because they come in between the exons. (genome.gov)
  • Introns are very large chunks of RNA within a messenger RNA molecule that interfere with the code of the exons. (genome.gov)
  • And these introns get removed from the RNA molecule to leave a string of exons attached to each other so that the appropriate amino acids can be encoded for. (genome.gov)
  • Dear Netters, I am working with different new genes of A. thaliana which are containing a relatively big number of introns (around 20) and unusual small exons. (bio.net)
  • So i am interested in all information about number of introns in A. thaliana genes and the smallest/biggest introns/exons. (bio.net)
  • Representation of intron and exons within a simple gene containing a single intron. (wikipedia.org)
  • Simple illustration of an unspliced mRNA precursor, with two introns and three exons (top). (wikipedia.org)
  • Re: What is intergenic DNA compared to introns and exons? (madsci.org)
  • Both terms, "introns" and "exons," were coined by Harvard biologist Walter Gilbert in 1978 (4) . (panspermia.org)
  • Introns were the functionless pieces that held the exons together. (panspermia.org)
  • Some sections of the gene coded for proteins and were called exons while intervening segments, called introns, did not seem to code for anything and were spliced out from the RNA message that was copied from the gene. (icr.org)
  • But most importantly, introns were found to play important roles in the alternative splicing of exons so that a single gene could produce literally tens to hundreds of different RNA and protein end products-like a Swiss army knife on steroids. (icr.org)
  • Here, leveraging population genomic data from Saccharomyces cerevisiae , Schizosaccharomyces pombe , and Lachancea kluyveri , we expose nonrandom patterns of genetic diversity in exons that border self-splicing introns. (genetics.org)
  • The GC-effect results in a higher GC content in minimal introns than their flanking exons as opposed to larger introns (≥125 nt) that always have a lower GC content than that of their flanking exons. (plos.org)
  • Mais l'epissage alternatif ne laisse pas des introns dans un ARNm mature, mais au contraire fait sauter des exons qui devraient etre pr sents. (futura-sciences.com)
  • Alternative splicing (AS) combines different transcript splice junctions that result in transcripts with shuffled exons, alternative 5 or 3 splicing sites, retained introns and different transcript termini. (futura-sciences.com)
  • 1. In the context of a new mammalian model organism recently sequenced and annotated, gene YFG has 3 introns and 4 exons. (biology-online.org)
  • The segments of our DNA that are commonly called "genes" consist of protein-coding exons and non-protein-coding introns. (blogspot.com)
  • how do I find the introns and exons? (protocol-online.org)
  • I have clicked on just about everything there is to click on, but I can't come up with the introns and exons in NCBI. (protocol-online.org)
  • Crystal structure of a self-splicing group I intron with both exons. (shapeways.com)
  • As an endonuclease it introduces a specific double-strand break at the junction of the two exons the cobA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. (rcsb.org)
  • Using a large set of plant gene sequences we compared individual introns to their flanking exons. (springer.com)
  • Both Zea mays and Arabidopsis thaliana introns are U-rich but display no apparent bias for A. We identified fifteen 11-mer U-rich motifs as frequent elements of maize introns, and these are virtually absent from exons. (springer.com)
  • Diagram of the location of introns and exons within a gene. (academickids.com)
  • Simple illustration of exons and introns. (academickids.com)
  • The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. (mdpi.com)
  • Most human genes contain multiple introns, necessitating mechanisms to effectively define exons and ensure their proper connection by spliceosomes. (elifesciences.org)
  • This synergy of 5' splice sites across introns and exons is likely important in promoting correct and efficient splicing of multi-intron pre-mRNAs. (elifesciences.org)
  • An intron can be recognized a) via cross-intron interactions leading directly to a catalytically active spliceosome, or b) via cross-exon interactions where the exons flanking an intron are first defined, after which cross-intron interactions between adjacent cross-exon complexes lead to spliceosome assembly ( Moldón and Query, 2010 ). (elifesciences.org)
  • Introns are removed from the pre-mRNA transcript by a protein complex called a spliceosome, and the protein-coding regions (called exons) are pasted together by another enzyme, RNA ligase. (evolutionnews.org)
  • These non-coding sequences, which are called introns, must be removed, and the remaining sequences-which are called exons-must then be joined together to produce a messenger RNA (mRNA) transcript that is ready to be translated into protein. (elifesciences.org)
  • The process of removing the introns and joining the exons is called splicing, and it is carried out by a molecular machine called the spliceosome. (elifesciences.org)
  • In the second step of splicing, the 5′ and 3′ exons are ligated together, and the intron is released ( 6 ). (asm.org)
  • The exons are shown as dashed lines with capital letters, and the intron is depicted as a plain line with lowercase letters. (asm.org)
  • We have tested this approach on three completely distinct biological problems: 1) prediction of protein three-dimensional folds, 2) discrimination between sequences of gene introns and exons, and 3) identification of putative RNA genes in genomic sequences. (nsti.org)
  • In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. (scirp.org)
  • Genes' introns and exons tell different stories here. (uncommondescent.com)
  • The human miR-33b sequence was introduced into intron 16 of mouse Srebf1 because miR-33b is located in intron 16 of human SREBF1 and there are high homologies in exons 16 and 17 between human and mouse. (ahajournals.org)
  • Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated regions (UTR), and nucleotides removed by RNA editing, in addition to introns. (wikipedia.org)
  • Apart from these three short conserved elements, nuclear pre-mRNA intron sequences are highly variable. (wikipedia.org)
  • In the cells of plants and animals, most gene sequences are broken up by one or more introns. (genome.gov)
  • RNA sequences called 'introns' promote heterochromatin structure formation. (eurekalert.org)
  • THE genes of complex organisms depend on introns to provide regulatory sequences that allow for accurate pre-mRNA processing and alternative splicing. (genetics.org)
  • A catalogue of known hemiascomycetous yeast splicing signals was then used as bait to screen the batch of selected coding sequences, and to validate or not the presence of an intron. (gsf.de)
  • b Compilation of intron sequences available at NCBI (release of June 2001). (gsf.de)
  • In contrast to bacteria which have no introns, eukaryotes (cells with a nucleus) have introns which are intervening sequences within genes which get spliced out when genes are transcribed and are not expressed in the protein. (madsci.org)
  • One possibility is, "Introns originated to circumvent the problem of the random distribution of stop codons in random primordial sequences" (6) . (panspermia.org)
  • Because the neutral model theory of evolution needed lots of junk in the genome to provide mutational fodder to somehow magically spit out new and useful DNA sequences for the mystical forces of selection to act upon, introns were promptly plopped in the neutral DNA or junk category. (icr.org)
  • Here, we show that, after positive selection, hCD2 reporter expression from the Cd8a locus, which was generated by insertion of hCD2 cDNA into the first exon of the Cd8a gene, requires the incorporation of intron sequences into the hCD2 transcript. (pnas.org)
  • Interestingly, stage-specific DNA demethylation was impaired in Cd8a reporter alleles that failed to express hCD2 in CD8 + T cells, and intron sequences lacking RNA splicing signals still restored hCD2 expression. (pnas.org)
  • A picture is beginning to emerge from a variety of organisms that for a subset of genes, the most important sequences that regulate expression are situated not in the promoter but rather are located within introns in the first kilobase of transcribed sequences. (frontiersin.org)
  • The size and sequence of introns in related species are not conserved and almost all of the sequences are evolving at the rate expected for neutral substitutions and fixation by drift. (blogspot.com)
  • Intron sequences are often littered with transposon and viral sequences that have inserted into the intron and this is not consistent with the idea that intron sequences are important. (blogspot.com)
  • In a comparison of the genomic sequences of homologous genes between C.elegans and Caenorhabditis briggsae for 26 GC-AG introns, the C at the +2 position is conserved in only five of these introns. (nih.gov)
  • This contrasting pattern may indicate that terminal introns and internal introns are differentially subject to hypothesized selection pressures modulating intron size and provides further evidence of widespread selective constraints on noncoding sequences. (broadinstitute.org)
  • Imagine that the initial RNA derived from its DNA template has the organization A-B-C-D-E-F, where the letters represent blocks that specify amino acid sequences and the dashes in between the letters stand for introns. (blogspot.com)
  • Back in my days doing sequence alignments to examine phylogenetic relationships among primates, I recall 'discovering' that there were conserved sequences in introns, typically near their beginnings and ends. (blogspot.com)
  • Both teams have proposed a mechanism whereby the sequences clutter up the spliceosome apparatus and thereby prevent it from splicing newly transcribed introns. (the-scientist.com)
  • Brown JWS: A catalogue of splice junction and putative branch point sequences from plant introns. (springer.com)
  • Carle-Urioste JC, Brendel V, Walbot V: A combinatorial role for exon, intron and splice site sequences in splicing in maize. (springer.com)
  • Csank C, Taylor FM, Martindale DW: Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. (springer.com)
  • Goodall GJ, Filipowicz W: The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. (springer.com)
  • Hanley BA, Schuler MA: Plant intron sequences: evidence for distinct groups of introns. (springer.com)
  • Dietrich RC, Incorvaia R, Padgett RA (1997) Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. (springer.com)
  • However, we find that the extent of self-splicing is greatly influenced by sequences flanking the intron and presumably reflects differences in the intron's ability to fold into an active conformation inside the cell. (asm.org)
  • We found that CAT activity is 5- to 300-fold higher when the transgene incorporates a hybrid intron than with an analogous transgene precisely deleted for the intervening sequences. (asm.org)
  • used intron 2 sequences. (uncommondescent.com)
  • examined the phylogenetic histories of chimp, macaque and human HLA-DRB1 genes again, but this time using sequences taken either from exon 2 or introns 1-4. (uncommondescent.com)
  • Surprisingly, the tree alignments using exon 2 or using introns 1-4 give markedly different pictures of the gene's phylogenetic history, even though both sets of sequences come from the very same genes. (uncommondescent.com)
  • It is clear that the intron sequences group according to species, whereas exon 2 sequences show no species-dependent relationships. (uncommondescent.com)
  • Others think that there has been cross-species shuffling of ancient peptide-binding motifs between different exon 2 sequences over time, but leaving the intron lineages unchanged. (uncommondescent.com)
  • It is not clear, however, how such a patchwork cross-species assortment of exon 2 sequences could have been acquired without disrupting the species-specific introns. (uncommondescent.com)
  • And the fact that the intron sequences do associate by species, with branch lengths as long or longer than the exon branch lengths, argues that many of these intronic lineages have been evolving independently for quite a while, indeed some as long as thirty to forty million years. (uncommondescent.com)
  • Is there any way of finding out where the intron/exon (exon-exon) boundaries are in a cDNA sequence? (bio.net)
  • Although splicing is closely coupled to several other processes during gene expression, it is still widely thought that the primary fitness benefits that introns confer to a species are through improved evolution via exon shuffling and increased proteome complexity by alternative splicing. (genetics.org)
  • In this article we present data that intron-containing genes produce more RNA and more protein than single-exon genes in yeast. (genetics.org)
  • The splicing patterns observed in the Arabidopsis mutants parallel those seen in mutations causing some human genetic disorders underlining the emerging similarities in mechanisms of splice site selection and intron/exon definition between plant and vertebrate systems. (nih.gov)
  • Analysis of the Arabidopsis intron mutations exhibiting complex splicing patterns will help to address fundamental questions in plant splicing, such as splice site selection and exon scanning. (nih.gov)
  • The introns-early theory is also called the exon theory of genes (3) . (panspermia.org)
  • Importantly, however, we show that exonic coconversion can only explain diversity gradients near intron-exon boundaries if the conversion template comes from outside the population. (genetics.org)
  • The exon/intron organisation of homologous nuclear genes was compared in several yeast species. (gsf.de)
  • I don't know why they think that the 1st intron comes before the 1st exon. (studentdoctor.net)
  • B. Draw a picture of YFG's most likely intron/exon organization. (biology-online.org)
  • I have also attached a picture of how I would draw YFG's intron/exon organization. (biology-online.org)
  • Further analysis of 47 GT47 genes in maize revealed that they can divide into five clades with diverse exon-intron structures. (springer.com)
  • This vector expresses human CD33 (Exon 1-7) cDNA with the native introns 1 and 2 within the sequence. (addgene.org)
  • Computer model showing the structure of a self-splicing group I intron (cyan) with a small human nucleoprotein (purple) and two exon fragments (yellow, orange). (sciencephoto.com)
  • Human spliceosome assembly involves both cross-intron and cross-exon interactions, but how these work together is unclear. (elifesciences.org)
  • We examined in human nuclear extracts dynamic interactions of single pre-mRNA molecules with individual fluorescently tagged spliceosomal subcomplexes to investigate how cross-intron and cross-exon processes jointly promote pre-spliceosome assembly. (elifesciences.org)
  • However, the mechanisms by which cross-intron and cross-exon pre-spliceosomes work together to facilitate pre-mRNA splicing remain unclear. (elifesciences.org)
  • A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. (mdpi.com)
  • The 5′ splice site is determined by the P1 helix, which is formed by base pairing between the internal guide sequence of the intron and the last 6 nucleotides (nt) of the 5′ exon. (asm.org)
  • At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. (scirp.org)
  • Subsequently, based on the po-sition frequencies of four kinds of bases in regions near intron/coding exon boundary, initia-tion and termination site of translation, 12 position parameters are selected as diversity source. (scirp.org)
  • Exon 2 comparisons typically showed cross-species associations, while intron comparisons showed within-species associations. (uncommondescent.com)
  • It's not that exon 2 is highly variable and the introns are more conserved, because this is not the case. (uncommondescent.com)
  • Rather, the intron lineages group together according to species, while the exon 2 lineages do not. (uncommondescent.com)
  • Does the intron/exon structure of eukaryotic genes belie their ancient assembly by exon-shuffling or have introns been inserted into preformed genes during eukaryotic evolution? (semanticscholar.org)
  • An intron (for intragenic region) is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. (wikipedia.org)
  • The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. (wikipedia.org)
  • However, different types of introns were identified through the examination of intron structure by DNA sequence analysis, together with genetic and biochemical analysis of RNA splicing reactions. (wikipedia.org)
  • In addition, they contain a branch point, a particular nucleotide sequence near the 3' end of the intron that becomes covalently linked to the 5' end of the intron during the splicing process, generating a branched (lariat) intron. (wikipedia.org)
  • Human genes are on average interrupted about 10 times, and the introns typically contain about 90 percent of the DNA sequence in the whole gene. (genome.gov)
  • An intron is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. (wikipedia.org)
  • After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom). (wikipedia.org)
  • These mutations illustrate the complexity of the splicing reaction (where the final splicing event reflects the characteristics such as splice site sequence, intron size and composition, and their interactions with spliceosomal components) and how single nucleotide mutations can affect the strength and balance of interactions to alter splicing patterns. (nih.gov)
  • An intron is a non-coding sequence in a gene . (wikipedia.org)
  • After the introns have been removed (bottom), the mature mRNA sequence is ready for translation . (wikipedia.org)
  • In the cases herein illustrated, some intron positions were found divergent in homologues sharing a high degree of sequence conservation, suggesting that these positions may result either from intron sliding or intron gain events [Bon et al. (gsf.de)
  • This would imply the existence of very accurate and reliable mechanism, distinct from the Fink system previously cited, capable of spotting an intron in the ORF sequence, and of removing it without introducing frame reading errors. (gsf.de)
  • Fifth, intron GC content and sequence divergence tend to have an adverse correlation [20] . (plos.org)
  • We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation. (frontiersin.org)
  • These patterns suggest that long introns as well as extremely short introns in this unusually intron-rich fungal genome are in mutation-selection disequilibrium and that the proportion of constrained functional sequence in introns does not scale linearly with size. (broadinstitute.org)
  • We find that untranslated region introns are longer than coding-region introns and that first introns are substantially longer than subsequent introns, suggesting heterogeneous distribution of constrained functional sequence and/or selective pressures on intron size within genes. (broadinstitute.org)
  • These so-called introns are typically spliced out from their original sequence between transcription and translation and rapidly destroyed prior to protein production. (the-scientist.com)
  • Mitochondrial DNA endonuclease and mRNA maturase involved in intron homing and required for splicing of the cytochrome b (cobA) gene intron, containing its own coding sequence. (rcsb.org)
  • Spliceosomes are precise molecular 'scissors' that can recognize where a coding module stops and an intron starts, and then make a snip in the pre-mRNA to remove the non-coding sequence. (elifesciences.org)
  • This structure is achieved by base-pairing interactions throughout the intron sequence forming RNA helices, which then fold into a specific conformation to create a catalytic core within the intron. (asm.org)
  • If we analyze the computed secondary structures of the RPS17B, RPS6B and APE2 wildtype introns we can easily identify stable stems whose 3' and 5' constituents are close to the donor site and the branchpoint sequence (Figure 9). (nih.gov)
  • The open reading frames (ORFs) specifying group II intron-encoded proteins, when present, are located in the loop region of the structural domain IV, with most of the coding sequence outside the intron catalytic core. (asmscience.org)
  • There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. (asmscience.org)
  • Retrohoming is mediated by a ribonucleoprotein particle that contains the intron-encoded protein and excised intron RNA, with target specificity determined largely by base pairing of the intron RNA to the DNA target sequence. (utexas.edu)
  • They appear to be related to group II introns, and possibly to spliceosomal introns. (wikipedia.org)
  • Organellar group II introns are considered to be the ancestors of nuclear spliceosomal introns. (pnas.org)
  • Search for information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. (pitt.edu)
  • This database contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae, such as known spliceosomal introns in the yeast genome and documented the splice sites actually used. (pitt.edu)
  • Alioto TS (2007) U12DB: a database of orthologous U12-type spliceosomal introns. (springer.com)
  • Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. (asmscience.org)
  • It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. (asmscience.org)
  • The recent origins of spliceosomal introns revisited. (semanticscholar.org)
  • The phylogenetic distribution of spliceosomal introns continues to strongly favor the intronslate theory. (semanticscholar.org)
  • Origin of spliceosomal introns and alternative splicing. (semanticscholar.org)
  • These features, as well as structural similarities with nuclear introns, have led to the proposition that ancestors of modern group II introns have crossed kingdoms from prokaryotes to eukaryotes via eubacterial endosymbionts, and eventually evolved into nuclear introns ( 2 ). (pnas.org)
  • Given the extensive coupling of splicing with mRNA metabolism, it is not surprising that removing the introns from genes in higher eukaryotes (where intron-containing genes predominate) disrupts mRNA synthesis and often lowers cytoplasmic mRNA levels. (genetics.org)
  • Bacteria have no introns, and single-celled eukaryotes have very few because they lost them in later evolutionary stages. (panspermia.org)
  • However, despite all of the amazing discoveries made concerning the introns of plants and animal genes, some evolutionists still speculated that perhaps introns in more seemingly simple one-celled eukaryotes, were still unnecessary and useless products of random evolution. (icr.org)
  • Evidence in plants so far indicates that splicing signals of plant U12 introns and their splicing machinery are similar to U12 intron splicing in other eukaryotes. (springer.com)
  • Introns are segments of genes, found in eukaryotes, that do not code for proteins. (evolutionnews.org)
  • The introns of higher eukaryotes can often be very long indeed - in many cases spanning hundreds of thousands or even millions of bases. (evolutionnews.org)
  • Lower eukaryotes (for example, yeast) tend to have shorter and fewer introns. (evolutionnews.org)
  • Thus far, however, efficient group II intron-based gene targeting reactions have not been demonstrated in eukaryotes. (utexas.edu)
  • For example, introns are extremely common within the nuclear genome of jawed vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms, for example baker's/brewer's yeast (Saccharomyces cerevisiae). (wikipedia.org)
  • As there are no other candidates for RNA processing factors in the well-described and small chloroplast genome, it was suggested that matK is responsible for splicing these introns. (pnas.org)
  • The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. (genetics.org)
  • The small and compact yeast genome only contains about 295 introns, and scientists were able to systematically delete each of them and then observe the effects on yeast growth. (icr.org)
  • In fact, the whole intron system in yeast genes provides an ingenious mechanism of engineered adaptability in the genome. (icr.org)
  • Following cleavage of the intron-free homing site, the intron-containing copy of the mitochondrial genome is used as a template for homologous recombination (HR), resulting in the conversion of an intron-free to an intron-containing locus. (genetics.org)
  • Here we analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations) from the data released by the 1000 Genome Project to study the size dynamics of minimal introns. (plos.org)
  • However, expression-controlling introns can be identified computationally in species with relatively small introns, based on genome-wide differences in oligomer composition between promoter-proximal and distal introns. (frontiersin.org)
  • The genes regulated by introns are often expressed in most tissues and are among the most highly expressed in the genome. (frontiersin.org)
  • In fact, certain introns may be the primary element directing the expression of some of the most highly expressed genes in the genome, causing the gene to be constitutively activated like a car with a heavy brick on its accelerator. (frontiersin.org)
  • About 245/295 of the remaining introns in yeast have been artificially removed by researchers who are constructing an artificial yeast genome suggesting that over 80% of the introns that survived evolutionary loss are also junk [ Yeast loses its introns ]. (blogspot.com)
  • Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. (frontiersin.org)
  • In this review, we provide a brief overview of what is presently known about group II introns, including RmInt1 in particular, in the context of their possible contribution to S. meliloti genome evolution. (frontiersin.org)
  • We conducted a genome-wide analysis of the roles of mutation and selection in sculpting intron size in the fungal pathogen Cryptococcus neoformans. (broadinstitute.org)
  • There is a single H2A gene in the genome of A. nidulans, and it contains three introns. (nih.gov)
  • At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. (blogspot.com)
  • To assess the potential biological role of these unusually stable introns, the team used CRISPR to delete a handful of them from the yeast genome, and compared the growth of the altered cells to normal cells by culturing them together. (the-scientist.com)
  • Elela's group found that many introns across the yeast genome-around 90 percent-had this effect when deleted. (the-scientist.com)
  • Group I introns may also insert into the natural intron insertion site at the RNA level, and subsequently become stably integrated into the host genome. (biomedsearch.com)
  • It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. (harvard.edu)
  • Our results indicate that a substantial fraction (66%) of the reduction in intron size as well as in genome size had already occurred in nonflying archosaurs. (harvard.edu)
  • Using phylogenetically independent contrasts, we found that the proposed inverse correlation of genome size and basal metabolic rate (BMR) is significant among amniotes and archosaurs, whereas intron and genome size variation within birds showed no significant correlation with BMR. (harvard.edu)
  • These results suggest that the contrast between genome size/BMR and intron size/BMR correlations may be a consequence of different intensities of selection for these traits and that we should not expect changes in intron size to be significantly associated with metabolically costly behaviors such as flight. (harvard.edu)
  • Saccharomyces cerevisiae possesses a compact genome, containing only 295 introns which are found across 280 genes (Hooks et al . (evolutionnews.org)
  • Here we show that the physical presence of introns in the genome promotes cell survival under starvation conditions . (evolutionnews.org)
  • Elela and his team determined that approximately 90 percent of introns across the genome of Saccharomyces had this result when removed. (evolutionnews.org)
  • Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns. (asmscience.org)
  • Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. (semanticscholar.org)
  • In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. (wikipedia.org)
  • On the other extreme, a recent study suggests that the shortest known eukaryotic intron length is 30 base pairs (bp) belonging to the human MST1L gene. (wikipedia.org)
  • Richard Roberts' and Phil Sharp's labs showed that eukaryotic genes contain many interruptions, called introns. (genome.gov)
  • Introns are interruptions in the text of eukaryotic genes. (panspermia.org)
  • Recent studies of entire eukaryotic genomes have now shown that the lengths and density (introns/gene) of introns varies considerably between related species . (wikipedia.org)
  • Introns are ubiquitous in eukaryotic transcripts. (blogspot.com)
  • In the past few years, sequencing advances and our ability to delete introns from eukaryotic genomes have started to provide answers to some of these questions. (blogspot.com)
  • Introns exist mainly (but not only) in eukaryotic cells . (academickids.com)
  • Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. (mdpi.com)
  • Introns are ubiquitous features of all eukaryotic cells. (evolutionnews.org)
  • This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. (asmscience.org)
  • Methodology/Principal Findings: By using a plasmid-based Xenopus laevis oocyte microinjection assay, we show that group II intron RNPs can integrate efficiently into target DNAs in a eukaryotic nucleus, but the reaction is limited by low Mg2+ concentrations. (utexas.edu)
  • In order to use group II introns to manipulate eukaryotic genomes, the catalytically active ribonucleoprotein (RNP) particles must be expressed. (ideaconnection.com)
  • the mRNA miss large gaps called introns. (genome.gov)
  • After RNA is transcribed from DNA, the introns are cut out before the mRNA is translated into protein. (genome.gov)
  • The spliceosome, which removes introns from the coding mRNA, is a large cellular complex containing hundreds of proteins and at least five small nuclear RNAs. (genetics.org)
  • The question arises: Are the introns directly responsible for increasing gene expression or does their removal act indirectly, by simply derailing the mRNA synthesis assembly line? (genetics.org)
  • We further show that genetic deletion of introns from yeast genes decreases mRNA production, and in two cases of three we show that intron removal causes a phenotypic growth defect. (genetics.org)
  • Arabidopsis intron mutations and pre-mRNA splicing. (nih.gov)
  • A spliceosome removes introns from a transcribed pre- mRNA segment (top). (wikipedia.org)
  • The ability of some introns to strongly stimulate mRNA accumulation from several hundred nucleotides downstream of the transcription start site, even when the promoter has been deleted, reveals that our understanding of gene expression remains incomplete. (frontiersin.org)
  • This article focuses on the specific kind of intron that increases mRNA accumulation because these introns seem to play a major role in regulating the gene in which they are located and because their effects are difficult to fit into our current understanding of gene expression. (frontiersin.org)
  • Introns are divided according to their mechanism of excision: group I and group II introns, pre-mRNA introns, tRNA introns and the HAC1 intron. (pitt.edu)
  • For nuclear pre-mRNA introns, transcription frequencies, as determined by microarray experiments, have also been included. (pitt.edu)
  • Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. (blogspot.com)
  • Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. (mit.edu)
  • GC-AG introns represent 0.7% of total human pre-mRNA introns. (nih.gov)
  • If you follow his logic, 90% of the introns end up in one or another mature mRNA. (blogspot.com)
  • Intron enhances stability of mRNA. (addgene.org)
  • Goodall GJ, Filipowicz W: Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. (springer.com)
  • Introns are sections of DNA within a gene that do not encode part of the protein that the gene produces, and are spliced out of the mRNA that is transcribed from the gene before it is exported from the cell nucleus . (academickids.com)
  • Before it can serve as a template to create a protein, this pre-mRNA must be processed and all the introns removed by a structure called the spliceosome. (elifesciences.org)
  • When a pre-mRNA has several introns, a spliceosome assembles anew for each of them. (elifesciences.org)
  • The experiments show that spliceosomes working on different introns in the same pre-mRNA actually help each other out. (elifesciences.org)
  • This effect of introns on growth is not linked to the expression of the host gene, and was reproduced even when translation of the host mRNA was blocked. (evolutionnews.org)
  • We show that U6atac level depends on both RNA polymerases II and III and can be rapidly increased by cell stress-activated kinase p38MAPK, which stabilizes it, enhancing mRNA expression of hundreds of minor intron-containing genes that are otherwise suppressed by limiting U6atac. (elifesciences.org)
  • The resulting higher levels of U6atac promoted splicing of the introns in its target mRNA transcripts, and also modulated various signaling pathways in the cells. (elifesciences.org)
  • E. Eden and S. Brunak, (2004) Analysis and recognition of 5'UTR intron splice sites in human Pre-mRNA, Nucleic Acids Res, 32, 1131-1142. (scirp.org)
  • Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae. (nih.gov)
  • Introns were first discovered in protein-coding genes of adenovirus, and were subsequently identified in genes encoding transfer RNA and ribosomal RNA genes. (wikipedia.org)
  • Whereas nuclear introns are removed by a large ribonucleoprotein complex called the spliceosome, each bacterial intron encodes a distinct maturase protein facilitating its splicing. (pnas.org)
  • Mining existing data from genomewide studies on yeast revealed that intron-containing genes produce more RNA and more protein and are more likely to be haplo-insufficient than nonintronic genes. (genetics.org)
  • Somehow, at some stage, introns have to be removed before the ultimate product of the gene, the protein, can be made without error. (panspermia.org)
  • At first, introns seemed to contain useless information that did not contribute to the final protein product created from an RNA template copied from a gene. (icr.org)
  • Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. (genetics.org)
  • Alternative splicing of introns within a gene allows a variety of protein isoforms from a single gene. (wikipedia.org)
  • These introns reveal a broad gap in our understanding of gene expression, and could be powerful tools for maximizing protein production in biotechnological and therapeutic applications. (frontiersin.org)
  • Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of nine group II introns in maize chloroplasts. (rcsb.org)
  • The introns are 51 nucleotides (nt), 56 nt and 50 nt in length and split codons for amino acids (aa) 18, 48 and 116 of the predicted protein. (nih.gov)
  • Since the discovery of introns in 1977 , researchers have proposed several theories why they exist: they could be important in regulating gene expression by delaying the amount of time it takes to translate DNA into protein, for instance. (the-scientist.com)
  • In support of this idea, additional experiments by Elela's group suggest that in starved cells, introns suppress the expression of ribosomal protein genes necessary for protein production. (the-scientist.com)
  • The protein stimulates the intrinsic ribozyme activity of the intron through binding to and stabilizing specific secondary and tertiary structure elements in the RNA. (rcsb.org)
  • Introns also sometimes contain "old code," sections of a gene that were probably once translated into protein but which are now discarded. (academickids.com)
  • We now report that DM2 is caused by a CCTG expansion (mean ∼5000 repeats) located in intron 1 of the zinc finger protein 9 ( ZNF9 ) gene. (sciencemag.org)
  • Purification and characterization of the SegA protein of bacteriophage T4, an endonuclease related to proteins encoded by group I introns. (asm.org)
  • Although not encoded by an intron, the bacteriophage T4 SegA protein shares common amino acid motifs with a family of proteins found within mobile group I introns present in fungi and phage. (asm.org)
  • Transcriptomic and genetic analyses indicate that introns promote resistance to starvation by enhancing the repression of ribosomal protein genes that are downstream of the nutrient-sensing TORC1 and PKA pathways . (evolutionnews.org)
  • Notably, introns could independently rescue the defects caused by intron deletion, even when their host protein was not produced (Fig. 3). (evolutionnews.org)
  • This protein is coded in group-II intron 2 of OXI3 (COX1). (uniprot.org)
  • Endonuclease activity of an intron-encoded protein was first shown for the yeast mtDNA introns aI1 and aI2. (asmscience.org)
  • Background: Mobile group II introns insert site-specifically into DNA target sites by a mechanism termed retrohoming in which the excised intron RNA reverse splices into a DNA strand and is reverse transcribed by the intron-encoded protein. (utexas.edu)
  • The introns-early theory, however, has claimed support from intron phase and protein structure correlations. (semanticscholar.org)
  • Upon further investigation, the team found 34 introns-around 11 percent of yeast introns-that appeared to be unusually stable and lingered around the spliceosome complex, the cellular machinery responsible for excising introns from pre-messenger RNA. (the-scientist.com)
  • U12 introns are removed from pre-mRNAs by a U12 intronspecific spliceosome. (springer.com)
  • Although this spliceosome shares many properties with the more abundant U2-dependent (U2) intron spliceosome, four of the five small nuclear RNAs (snRNAs) required for splicing are different and specific for the unique splicing of U12 introns. (springer.com)
  • As one assembles, this helps the spliceosome that processes the neighboring intron to get built. (elifesciences.org)
  • However, in addition to containing typical ('major') introns, several hundred human genes also contain a single 'minor' intron, and a minor spliceosome is needed to remove it. (elifesciences.org)
  • shed new light on the minor spliceosome by showing that a small non-coding RNA molecule known as U6atac, which catalyzes the removal of introns by the minor spliceosome, is highly unstable in human cells. (elifesciences.org)
  • This means that U6atac is a limiting factor for the splicing of minor introns-a process that is already limited by the very low abundance of the minor spliceosome under normal conditions. (elifesciences.org)
  • We have used the twin-ribozyme intron (Dir.S956-1) from the myxomycete Didymium iridis to test how a mobile group I intron containing a homing endonuclease gene (HEG) selects between potential insertion sites in the small subunit (SSU) rRNA in vitro, in Escherichia coli and in yeast. (biomedsearch.com)
  • Deleting a single intron reduces the capacity of cells to withstand nutrient depletion or starvation (Figs. 1, 2). (evolutionnews.org)
  • Thus, at least for highly expressed genes, transcription of long introns, which are particularly common in mammals, is costly. (nih.gov)
  • All land plant chloroplasts with the exception of some parasitic species in the genus Cuscuta ( 4 , 5 ) contain a single maturase gene called matK in the intron of the lysine tRNA-K(UUU) gene. (pnas.org)
  • Applied methods to find introns in homologous genes as well as new ones in the 7 related species. (gsf.de)
  • S. cerevisiae homologues, identified through BLAST comparisons, were collected in each of the seven yeast species, and compared to an updated and non-redundant catalogue of S. cerevisiae genes containing intron . (gsf.de)
  • When scientists discovered that one primordial species, a photosynthetic cyanobacterium named Fischerella, has introns, both camps claimed that the new evidence supported their view (2) . (panspermia.org)
  • But Nobel prize-winner Renato Dulbecco, for one, says that the introns couldn't have been added late, because there are too many similarities among the introns found in species that diverged too long ago (7) . (panspermia.org)
  • In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. (genetics.org)
  • There have been several comparative studies within and among species, revealing situations where short introns (or minimal introns) are under selection, and most of them have focused on model organisms, such as Drosophila. (plos.org)
  • Many species have lost introns or reduced their lengths drastically suggesting that the presence of large introns can be detrimental in some cases (probably large populations). (blogspot.com)
  • Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. (frontiersin.org)
  • These mobile introns are self-splicing RNAs and retroelements, which are highly abundant in S. meliloti and, to a lesser extent, in closely related species. (frontiersin.org)
  • We would be surprised if yeast could be the only species that have a use for these excised introns. (the-scientist.com)
  • The amount of intron DNA varies widely between species . (academickids.com)
  • The pufferfish species Fugu rubripes has a very low amount of intron DNA, whereas related species have higher amounts. (academickids.com)
  • In the introns-early model ancestral genes are believed to have included a large number of introns, some of which have been lost over evolutionary time, leading to the different but similar intron patterns in related genes of different species. (academickids.com)
  • The introns-late model suggests instead that introns occur in the same location in variants of a given gene because the location is in some way predisposed to the introduction of an intron, and therefore that a similar intron pattern may arise in two different species by a form of convergent evolution . (academickids.com)
  • These differences explain the relative stability of the circular species, demonstrate how it is prone to react with a target molecule for circle integration and thus supports the notion that the circular form is a biologically significant molecule possibly with a role in intron mobility. (mdpi.com)
  • the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. (biomedsearch.com)
  • Our results suggest that reverse splicing, in addition to the established endonuclease-mediated homing mechanism, potentially accounts for group I intron spread into the homologous sites of different strains and species. (biomedsearch.com)
  • rpl16 intron and trnD-trnY-trnE-trnT spacers, with the goals of evaluating 1) the delimitation of species and 2) Gould's hypotheses for the origin of species and infraspecific taxa. (bioone.org)
  • The group II intron LtrB is a ribozyme that catalyzes its own splicing and is able to insert itself into essentially any gene in various species. (ideaconnection.com)
  • ABSTRACT: Amongst endonuclease, the homodimeric variety is found in many prokaryotes for processing of the introns out from pre-RNAs. (scirp.org)
  • To investigate the role that introns may play in cellular fitness we studied their genetic contribution to the fitness of Saccharomyces cerevisiae . (genetics.org)
  • Search for information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. (pitt.edu)
  • About 98% of the introns in modern yeast ( Saccharomyces cerevisiae ) have been eliminated during evolution form a common ancestor that probably had about 18,000 introns [ Yeast loses its introns ]. (blogspot.com)
  • I'd like to see Sternberg's math on what percentage of the nucleotides within introns are actually employed in facilitating splicing. (blogspot.com)
  • 2011). Most of these introns are shorter than 500 nucleotides in length and only nine yeast genes possess more than one intron (Neuvéglise et al . (evolutionnews.org)
  • Group II introns are highly structured ribozymes, found in bacteria and organellar genomes of plants, fungi, protists, and some animals. (pnas.org)
  • Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. (frontiersin.org)
  • Some introns such as Group I and Group II introns are actually ribozymes that are capable of catalyzing their own splicing out of the primary RNA transcript. (academickids.com)
  • The intron harbours two ribozymes that have the potential to linearize the circle. (mdpi.com)
  • Group II introns: ribozymes that splice RNA and invade DNA, p 469-505. (asmscience.org)
  • Group II introns: mobile ribozymes that invade DNA. (asmscience.org)
  • The frequency of introns within different genomes is observed to vary widely across the spectrum of biological organisms. (wikipedia.org)
  • In organisms with large genomes, introns are indispensable for the process of alternative splicing, which is essential for regulating gene expression and function. (blogspot.com)
  • Why would single cells with compact genomes tolerate the energetic cost of transcribing, splicing, and degrading introns if their only function is associated with the act of their removal? (blogspot.com)
  • U12-dependent (U12) introns have persisted in the genomes of plants since the ancestral divergence between plants and metazoans. (springer.com)
  • Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. (mdpi.com)
  • Invention Description Our invention enables high-throughput screening of genomes for the purpose of targeted modifications of DNA with the LI.LtrB group II intron (targetron). (ideaconnection.com)
  • Darwinists responded to the discovery of introns by guessing that they arose either early or late. (panspermia.org)
  • The discovery of introns led to the Nobel Prize in Physiology or Medicine in 1993 for Phillip Sharp and Richard Roberts . (wikipedia.org)
  • The discovery of introns' function in yeast was reached independently by Elela's team and another research group via different approaches. (the-scientist.com)
  • Selection for short introns in highly expressed genes. (nih.gov)
  • Thus, natural selection appears to favor short introns in highly expressed genes to minimize the cost of transcription and other molecular processes, such as splicing. (nih.gov)
  • Last, adaptive and purifying selection can work together to keep the lengths of short introns around an optimum size [19] . (plos.org)
  • Introns are found in the genes of most organisms and many viruses and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA) and transfer RNA (tRNA). (wikipedia.org)
  • When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. (wikipedia.org)
  • Transfer RNA introns that depend upon proteins for removal occur at a specific location within the anticodon loop of unspliced tRNA precursors, and are removed by a tRNA splicing endonuclease. (wikipedia.org)
  • Bacterial group II introns encode maturase proteins required for splicing. (pnas.org)
  • Using data on the expression of genes that encode proteins in Caenorhabditis elegans and Homo sapiens, we show that introns in highly expressed genes are substantially shorter than those in genes that are expressed at low levels. (nih.gov)
  • Introns would also allow for alternative splicing, a process that allows ribosomes to assemble multiple different proteins from a single gene. (the-scientist.com)
  • The discovery of the RNA self-splicing group I intron provided the first demonstration that not all enzymes are proteins. (shapeways.com)
  • Introns sometimes allow for alternative splicing of a gene, so that several different proteins that share some sections in common can be produced from a single gene. (academickids.com)
  • Each of these intron-encoded proteins is thought to initiate the homing of its own intron by cleaving the intronless DNA at or near the site of insertion. (asm.org)
  • Introns need to be removed from nascent messenger RNA through the process of splicing to produce functional proteins. (evolutionnews.org)
  • This intron catalyzes its own excision from precursor 23S rRNAs without the aid of proteins by a well-characterized two-step pathway (Fig. 1 ) ( 6 ). (asm.org)
  • While the role of group I and group II intron-encoded proteins in homing has been well defined, the function of these proteins in intron dissemination to new sites remains the subject of intense study. (asmscience.org)
  • These mobile introns, their intron-encoded proteins, and the mechanisms by which mobility occurs are the subject of this chapter. (asmscience.org)
  • Of the three activities of the group II intron-encoded proteins, the maturase domain is present in all known cases. (asmscience.org)
  • Basic research into the structure and function of intron-encoded proteins and of the dynamics of mobility pathways is yielding a refined view of their modus operandi. (asmscience.org)
  • The fact that genes were split or interrupted by introns was discovered independently in 1977 by Phillip Allen Sharp and Richard J. Roberts, for which they shared the Nobel Prize in Physiology or Medicine in 1993. (wikipedia.org)
  • A surprising phenomenon was discovered in 1977 - introns. (panspermia.org)
  • Introns were first identified in 1977 by the lab of Richard Roberts and Phil Sharp (Chow et al . (evolutionnews.org)
  • And now one of the pet darlings of junk DNA speculation, the alleged useless nature of introns (intervening noncoding pieces of genes), has also been tossed in the evolutionary trash heap. (icr.org)
  • These results indicate that while the majority of GC-AG introns appear to be constitutively spliced and have no evolutionary constraints to prevent them from being GT-AG introns, a subset of GC-AG introns is involved in alternative splicing and the C at the +2 position of these introns can have an important role in splicing regulation. (nih.gov)
  • There are two competing theories as to the evolutionary origin of introns, which is usually studied in a highly conserved family of genes such as the actins . (academickids.com)
  • Burge CB, Padgett RA, Sharp PA (1998) Evolutionary fates and origins of U12-type introns. (springer.com)
  • Our results reveal functions of introns that may help to explain their evolutionary preservation in genes, and uncover regulatory mechanisms of cell adaptations to starvation. (evolutionnews.org)
  • We propose that minor introns are embedded molecular switches regulated by U6atac abundance, providing a novel post-transcriptional gene expression mechanism and a rationale for the minor spliceosome's evolutionary conservation. (elifesciences.org)
  • DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. (asmscience.org)
  • Parallels between these results and previously observed protection of 16S ribosomal RNA by aminoglycosides raise the possibility that group I intron splicing and transfer RNA selection by ribosomes involve similar RNA structural motifs. (sciencemag.org)
  • Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA. (biomedsearch.com)
  • Introns can also encode RNA molecules such as microRNAs (which are required for the expression of mRNAs during development) and small nucleolar RNAs (which play an important role in the processing of ribosomal RNAs) (e.g. (evolutionnews.org)
  • and secondly, loss of chloroplast translation leads to loss of splicing for some, but not all chloroplast introns, suggesting that a chloroplast reading frame is required for splicing these multiple introns ( 7 , 15 , 16 ). (pnas.org)
  • This teamwork is likely important to guarantee that multiple introns are cut out quickly and accurately. (elifesciences.org)
  • Arabidopsis intron mutants provide and will continue to provide a valuable source of information on in vivo plant intron splicing. (nih.gov)
  • Search algorithms of AS forms in a variety of Arabidopsis databases showed they contained an unusually high fraction of retained introns (above 30%), compared with 10%that was reported for humans. (futura-sciences.com)
  • Thus, retained introns are a prominent feature of AS in Arabidopsis and as such may play a regulatory function. (futura-sciences.com)
  • The CRS2 surface corresponding to the putative tRNA binding face of PTH is considerably more basic than in PTH, suggesting that CRS2 interacts with group II intron substrates via this surface. (rcsb.org)
  • Kjems, J., Leffers, H., Olsen,T. and Garrett, R.A. (1989) A unique tRNA intron in the variable loop of the extreme thermophile Thermophilum pendens and its possible evo- lutionary implications. (scirp.org)
  • In other words, introns are non-coding regions of an RNA transcript, or the DNA encoding it, that are eliminated by splicing before translation. (wikipedia.org)
  • We validated the unique mutation dynamics of minimal introns in keeping their near-optimal size and GC content, and our observations suggest potentially important functions of human minimal introns in transcript processing and gene regulation. (plos.org)
  • The preponderance of retained introns (65%) were either part of open reading frames, present in the UTR region or present as the last intron in the transcript, indicating that their occurrence would not participate in non-sense-mediated decay. (futura-sciences.com)
  • Focus on the difference between a transcript and an intron. (blogspot.com)
  • I just read the 'Let's do the math again' post, and Sternberg reminds everyone that although he can perform the operations correctly, he still doesn't get the difference between a transcript and an intron. (blogspot.com)
  • In the context of the pre-rRNA transcript, the intron folds into a complex tertiary structure, forming an active site for phosphodiester transfer. (asm.org)
  • Numerous plastid endo- and exoribonuclease-sensitive sites within genes, introns, and intergenic regions imply their complex and important role in governing transcript degradation, thus determining transcript half-lives. (plantphysiol.org)
  • Introns are now known to provide a reservoir of small noncoding (nc)RNAs that act in trans on other genes. (blogspot.com)
  • It is the presence of introns that makes this permutative expansion of messenger RNAs possible in the first place. (blogspot.com)
  • Andersen KL, Beckert B, Masquida B, Johansen SD, Nielsen H. Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock. (mdpi.com)
  • In multicellular organisms most genes contain at least one intron, usually more. (genetics.org)
  • Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. (reactome.org)
  • 2019. Introns are mediators of cell response to starvation. (icr.org)
  • 2019) [ Yeast loses its introns ]. (blogspot.com)
  • Parenteau, J., and Elela, S. A. (2019) Introns: Good Day Junk Is Bad Day Treasure. (blogspot.com)
  • There is, however, no consensus that introns serve to increase gene expression. (genetics.org)
  • In contrast, the density of introns in a gene does not strongly depend on the level of gene expression. (nih.gov)
  • One example is the surprisingly large effect that some introns have on gene expression. (frontiersin.org)
  • However, introns are also preserved in organisms where alternative splicing and splicing-dependent regulation of gene expression are rare. (blogspot.com)
  • This chapter compares U12 and U2 splicing and reviews what is known about plant U12 introns and their possible role in gene expression. (springer.com)
  • A generic intron increases gene expression in transgenic mice. (asm.org)
  • To investigate the role of splicing in the regulation of gene expression, we have generated transgenic mice carrying the human histone H4 promoter linked to the bacterial gene for chloramphenicol acetyltransferase (CAT), with or without a heterologous intron in the transcription unit. (asm.org)
  • These two types of introns represent different ways in which selfish elements exploit functions that promote their invasiveness. (asmscience.org)
  • A large-scale bioinformatics analysis revealed the origin and evolution of GT47 gene family, and identified two clades of intron-poor genes with putative functions in drought stress responses and seed development in maize. (springer.com)
  • According to in-silico screening prediction data, putative ARE1, ARE2 and ARE3 are located within GNMT intron 1, and ARE4 is located within intron 2. (aacrjournals.org)
  • The antibiotics also disrupted structural contacts that have been proposed to bring the 5' cleavage site of the intron into proximity to the catalytic core. (sciencemag.org)
  • About iNtRON Bio iNtRON Bio is a biotechnology company in Korea focused on the development of bacteriophage/endolysin-based novel anti-bacterials for the treatment of serious and life-threatening infections caused by multidrug-resistant bacteria. (prnewswire.com)
  • Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. (asmscience.org)
  • Pre-spliceosomes can form on multi-intron pre-mRNAs through at least two different pathways. (elifesciences.org)
  • These intron effects appear to couple the TOR and PKA pathways to the repression of ribosome biogenesis, on the basis of nutrient concentration (Fig. 6 and Extended Data Fig. 10b, c). (evolutionnews.org)
  • Intron splicing pathways and structures. (asmscience.org)
  • Therefore, the scientists also grew the various intron-deletion strains of yeast under nutrient stressed environments and were shocked to discover that the introns were key to survival. (icr.org)
  • To find out, his group systematically constructed a library of 295 yeast strains in which each strain had a different intron deleted-a project the team started in 2002, Elela says. (the-scientist.com)
  • In this study, we present what is - to our knowledge - the first complete collection of yeast strains each with a deletion of a specific intron. (evolutionnews.org)
  • The researchers, led by Sherif Abou Elela of the University of Sherbrooke, systematically constructed a library of yeast strains, deleting a different intron from each of the 295 strains. (evolutionnews.org)
  • In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations. (genetics.org)
  • pre-rRNA of fungal and plant mitochondria -majority of chloroplast introns -several classes -require Mg 2+ -no cofactor. (slideserve.com)
  • Introns are now known to occur within a wide variety of genes throughout organisms and viruses within all of the biological kingdoms. (wikipedia.org)
  • We present a tool, keepme around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to reduce the number of false positives when detecting retention events. (caltech.edu)
  • It's unclear how the introns promote cell survival under starvation conditions. (the-scientist.com)
  • By mutagenesis, we show that the single U-rich motif in the Bronze2 intron of maize plays a key role in intron processing in vivo. (springer.com)
  • By analyzing the expression of hCD2 reporter from manipulated Cd8a alleles with distinct polyadenylation signal positions or intron structures defective in RNA splicing, we found that intron structures are essential for hCD2 expression in CD8 + T cells. (pnas.org)
  • I have had several replies about max length of introns (200kb? (bio.net)
  • 2006). It has also been shown that the length of introns (and, consequently, the time taken to transcribe them) can contribute to timing mechanisms during development (Swinburne and Silver, 2010). (evolutionnews.org)
  • These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast. (genetics.org)
  • To study the function of GC-AG introns in splicing regulation, 196 cDNA-confirmed GC-AG introns were identified in Caenorhabditis elegans. (nih.gov)
  • These represent 0.6% of the cDNA- confirmed intron data set for this organism. (nih.gov)
  • Our results suggest that inclusion of the generic intron in cDNA constructs may be valuable in achieving high levels of expression in transgenic mice. (asm.org)
  • Then, within the cell nucleus, specialized arrays of enzymes in complexes called spliceosomes locate the introns, snip them out, and splice the RNA back together. (panspermia.org)
  • In particular, the U1 snRNPs processing nearby introns collaborate to promote the assembly and activity of the spliceosomes. (elifesciences.org)
  • Minor introns occur in many highly conserved genes, but they are often inefficiently spliced. (elifesciences.org)
  • In vivo analysis of intron processing using splicing-dependent reporter gene assays. (springer.com)
  • Dietrich RC, Shukla GC, Fuller JD, Padgett RA (2001b) Alternative splicing of U12-dependent introns in vivo responds to purine-rich enhancers. (springer.com)
  • To address miR-33b function in vivo, we developed humanized mice, in which a miR-33b transgene is inserted within a Srebf1 intron. (ahajournals.org)
  • In organelles of photosynthetic land plants, most of the group II introns have lost the reading frames for maturases. (pnas.org)
  • Here, we show that the plastidial maturase MatK not only interacts with its encoding intron within trnK -UUU, but also with six additional group II introns, all belonging to intron subclass IIA. (pnas.org)
  • In addition, bacterial group II introns are mobile genetic elements. (pnas.org)
  • At least initially, the already existing splicing factors encoded by the invading group II introns, i.e., modified maturases, may have fulfilled this task. (pnas.org)
  • By contrast, domains required for the mobility of group II introns are missing in MatK. (pnas.org)
  • If true, MatK would be an example of a group II intron maturase that has left the strict association with just a single target intron, joined by the group I intron maturase BI4 from yeast mitochondria, which supports splicing of two group I introns ( 17 ). (pnas.org)
  • Group III introns are proposed to be a fifth family, but little is known about the biochemical apparatus that mediates their splicing. (wikipedia.org)
  • SGS is pleased to announce the acquisition of Intron Group, Sittard, NL. (sgs.com)
  • Here we report the X-ray crystal structure (3.1-A resolution) of a complete group I bacterial intron in complex with both the. (shapeways.com)
  • Aminoglycoside inhibitors of translation have been shown previously to inhibit in vitro self-splicing by group I introns. (sciencemag.org)
  • Domain Structure of a Group II Intron. (slideserve.com)
  • Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. (biomedsearch.com)
  • However, the frequency and general role of an RNA-based mobility pathway in the spread of natural group I introns is still unclear. (biomedsearch.com)
  • Here we evaluate the self-splicing efficiency of group I introns from transcripts expressed by RNA polymerase II in human cells to directly measure ribozyme catalysis in a therapeutically relevant setting. (asm.org)
  • The group I intron from Tetrahymena thermophila has served as a model system for studing both RNA catalysis and RNA folding ( 8 ). (asm.org)
  • Self-splicing reaction of the Tetrahymena group I intron. (asm.org)
  • Group I and group II introns are self-splicing elements with wide genomic distribution, reflecting their dispersal through active mobility mechanisms. (asmscience.org)
  • 2007. Bacterial group II introns: not just splicing. (asmscience.org)
  • Now on display: a gallery of group II intron structures at different stages of catalysis. (asmscience.org)
  • Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. (asmscience.org)
  • This feature enabled the development of mobile group II introns into bacterial gene targeting vectors ("targetrons") with programmable target specificity. (utexas.edu)
  • We also show that group II intron RNPs containing either lariat or linear intron RNA can introduce a double-strand break into a plasmid target site, thereby stimulating homologous recombination with a co-transformed DNA fragment at frequencies up to 4.8% of target sites. (utexas.edu)
  • However, by using similar RNP microinjection methods, we show efficient Mg2+-dependent group II intron integration into plasmid target sites in zebrafish (Danio rerio) embryos and into plasmid and chromosomal target sites in Drosophila melanogster embryos, indicating that DNA replication can mitigate effects of chromatinization. (utexas.edu)
  • Conclusions/Significance: Our results provide an experimental foundation for the development of group II intron-based gene targeting methods for higher organisms. (utexas.edu)
  • A self-splicing RNA excises an intron lariat. (asmscience.org)
  • 1997) Mol Cell Biol "Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. (wormbase.org)
  • Peg-Intron (peginterferon alfa-2b) Powder for Injection has been approved by the FDA as a once-weekly monotherapy for the treatment of chronic hepatitis C. It is indicated for patients with compensated liver disease who were not previously treated with alpha interferon. (centerwatch.com)
  • Peginterferon (PEG-INTRON, Schering Corporation, Kenilworth, NJ) is a new formulation of interferon recently approved for the treatment of HCV. (pharmacytimes.com)
  • In contrast to Drosophila, we find a positive correlation between d(N) and first intron or last intron length and a negative correlation between d(N) and internal intron length. (broadinstitute.org)
  • This splicing behaviour is in agreement with detailed splicing analyses of test plant introns. (nih.gov)
  • The high conservation of minor introns, typically one amidst many major introns in several hundred genes, despite their poor splicing, has been a long-standing enigma. (elifesciences.org)
  • Incorporation of the endogenous short intron structure and heterologous intron structure of the Cd4 locus restored hCD2 expression in mature CD8 + T cells in a variegated manner. (pnas.org)
  • Instead, our findings implicate intron mobility as a direct driver of host gene diversity. (genetics.org)
  • We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or nonrandom patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to empty target sites via homologous recombination. (genetics.org)
  • To assay the functional relevance of introns, a series of computational analyses and several detailed deletion studies were completed on the intronic genes of S. cerevisiae . (genetics.org)
  • It could be interpreted that the introns in S. cerevisiae are nucleic acid relics that have yet to be removed by evolution ( F ink 1987 ). (genetics.org)
  • In the absence of selection for intron retention, cycles of intron gain and loss ensue ( Goddard and Burt 1999 ), accompanied by recurrent endonuclease activity that predictably targets the very same recognition site. (genetics.org)
  • Frilander MJ, Steitz JA (1999) Initial recognition of U12-dependent introns requires both U11/5′ splice-site and U12/branchpoint interactions. (springer.com)
  • We further analyzed human minimal introns and minimal intron-containing genes (MIGs), and showed many their unique features, including non-random distribution among human chromosomes, tendency to reside near the 3′ end of transcripts, and higher expression level than other genes [14] . (plos.org)
  • Interestingly, the functional distribution of the transcripts with retained introns is skewed towards stress and external/internal stimuli-related functions. (futura-sciences.com)
  • A sampling of the alternative transcripts with retained introns were confirmed by RT-PCR and were shown to co-purify with polyribosomes, indicating their nuclear export. (futura-sciences.com)
  • Intron-containing expression cassettes were transfected into a human cell line, and RNA transcripts were analyzed for intron removal. (asm.org)
  • In support of this hypothesis, we show that the ability of the intron to fold and self-splice from cellular transcripts in vitro correlates well with the catalytic efficiency observed from the same transcripts expressed inside cells. (asm.org)
  • Since generation of functional ribosomes in T. thermophila depends on this rRNA processing event, it is not surprising that intron-containing precursor transcripts rapidly self-splice to completion in their native cellular environment ( 4 ). (asm.org)