Molecular Sequence Data
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.
RNA Splice Sites
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.
Amino Acid Sequence
Nucleic Acid Conformation
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.
Sequence Homology, Nucleic Acid
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.
RNA, Small Nuclear
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.
Sequence Analysis, DNA
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.
Sequence Homology, Amino Acid
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).
Open Reading Frames
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 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.
Polymerase Chain Reaction
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 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)
Ribonucleoproteins, Small Nuclear
RNA, Ribosomal, Self-Splicing
Ribonucleoprotein, U2 Small Nuclear
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.
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)
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.
Promoter Regions, Genetic
Nucleic Acid Precursors
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)
DNA Restriction Enzymes
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.
Repetitive Sequences, Nucleic Acid
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).
DNA Transposable Elements
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, Nucleic Acid
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).
RNA, Small Nucleolar
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.
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).
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.
5' Untranslated Regions
RNA Processing, Post-Transcriptional
Nucleic Acid Hybridization
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)
Expressed Sequence Tags
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 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.
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.
Exonic splicing enhancer
Short sequences of DNA are transcribed to RNA; then this RNA is translated to a protein. A gene located in the DNA will contain ... Part of the process of preparing the RNA includes splicing out the introns, sections of RNA that do not code for the protein. ... splice site of the intron to form the lariat. It is thought that SR proteins that bind to ESEs promote exon splicing by ...
Mitochondrial dicarboxylate carrier
Intron 1 of this gene has five short Alu sequences. Mitochondrial dicarboxylate carriers are dimers, each consisting of six ...
The positions of introns are conserved in all four human ENaC genes. The positions of the introns are also highly conserved ... The human gene SCNN1A is located in the short arm of chromosome 12 (12p3). Human SCNN1A includes 13 exons spanning about 29,000 ...
The human OTC gene is located on the short arm of chromosome X (Xp21.1). The gene is located in the Watson (plus) strand and is ... The open reading frame of 1,062 nucleotides and is disbused between 10 exons and nine introns. The encoded protein is 354 amino ...
Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on the proteins ... In other cases, expansions in the number of tandem repeats in exons or introns can cause disease. For example, the human gene ... Short, non-coding sequences that are repeated head-to-tail are called tandem repeats. Microsatellites consisting of 2-5 ... The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: ...
A short visit to Papua, video by Alastair Robinson and Davide Baj. Strange Fruits: A Garden's Chronicle, February 25, 2014. (in ... Molecular phylogeny of Nepenthaceae based on cladistic analysis of plastid trnK intron sequence data. Plant Biology 3(2): 164- ... Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molecular Phylogenetics and ...
Mir-281 microRNA precursor family
MicroRNA Xiong H, Qian J, He T, Li F (January 2009). "Independent transcription of miR-281 in the intron of ODA in Drosophila ... In molecular biology mir-281 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other ... mir-281 is found in an intron of the Drosophila ornithine decarboxylase antizyme (ODA) gene. Using the RACE technique the pri- ...
De novo genes are typically shorter and simpler in structure than most eukaryotic genes, with few if any introns. Over long ... Similarly, a gene's introns can be much larger than its exons. Regulatory regions can even be on entirely different chromosomes ... The sequences at the ends of the introns dictate the splice sites to generate the final mature mRNA which encodes the protein ... One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode ...
The second promoter region is found within the first intron and encodes a slightly shorter mRNA. This promoter contains ...
It is characterised by relatively few genes with very few introns. The genes are clustered together, with normally short ...
Tetratricopeptide repeat protein 39B
The genomic DNA is 136,517 bases long, consists of 39 introns and 20 exons, and is on the minus strand. The mRNA has a length ... The gene for TTC39B is located on the short arm of the ninth chromosome at 9p22.3. ... which results in a shorter protein. Isoform 3 and 4 have multiple differences in the central coding region but maintain the ... These differences cause translation initiation at an in-frame downstream AUG and results in isoform 5 having a shorter N- ...
Split gene theory
The exons of eukaryotes are generally short (human exons average ~120 bases, and can be as short as 10 bases) and introns are ... and possibly the intron splice enhancers that occur at the ends of introns, which aid in the removal of introns, the vast ... Based on the split gene theory, only genes split into short exons and long introns, with a maximum exon length of ~600 bases, ... It is anchored at an adenosine residue in intron between 10 and 50 nucleotides upstream of the 3' splice site. A short ...
Mir-708 microRNA precursor family
miR-708 is located on chromosome 11q14.1 and is endcoded in intron 1 of the ODZ4 gene. It is most highly expressed in the brain ... In molecular biology mir-708 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other ...
The third intron for the isoform 2 transcript is longer than the one found in isoform 1. The FAM71E1 transcript is regulated by ... Isoform 1 is 1281 bp long, and isoform 2 is slightly shorter at 1233 bp long. Both transcript variants have 5 exons, 4 of which ...
The short hairpin introns use splicing to bypass DROSHA cleavage, which is otherwise essential for the generation of canonical ... Mirtrons are a type of microRNAs that are located in the introns of the mRNA encoding host genes. Mirtrons arise from the ... Mirtrons arise from the spliced-out introns and are known to function like classical microRNAs (miRs) and regulate gene ... spliced-out introns and are known to function in gene expression. Mirtrons were first identified in Drosophila melanogaster and ...
Ponthier JL, Schluepen C, Chen W, Lersch RA, Gee SL, Hou VC, Lo AJ, Short SA, Chasis JA, Winkelmann JC, Conboy JG (May 2006). " ... Rbfox1, and the related protein Rbfox2, bind the consensus RNA sequence motif (U)GCAUG within introns to exert their functions ... Short, Sarah A.; Chasis, Joel A.; Winkelmann, John C.; Conboy, John G. (2006-03-14). "Fox-2 Splicing Factor Binds to a ... "Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16". The Journal ...
Rbfox2 and the related protein Rbfox1 bind to conserved (U)GCAUG RNA motifs in the introns adjacent to many alternatively ... Short, Sarah A.; Chasis, Joel A.; Winkelmann, John C.; Conboy, John G. (2006-03-14). "Fox-2 Splicing Factor Binds to a ... 2006). "Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16". J. ... Conserved Intron Motif to Promote Inclusion of Protein 4.1R Alternative Exon 16". Journal of Biological Chemistry. 281 (18): ...
In humans, the TP53 gene is located on the short arm of chromosome 17 (17p13.1). The gene spans 20 kb, with a non-coding exon 1 ... Furthermore, the usage of an internal promoter in intron 4 causes the ∆133 and ∆160 isoforms, which lack the TAD domain and a ... It is essential for the senescence response to short telomeres. WAF1/CIP1 encoding for p21 and hundreds of other down-stream ... McBride OW, Merry D, Givol D (January 1986). "The gene for human p53 cellular tumor antigen is located on chromosome 17 short ...
List of RNA-Seq bioinformatics tools
IsoInfer IsoInfer is a C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron ... Erne-Filter is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS- ... ABMapper BBMap Uses short kmers to align reads directly to the genome (spanning introns to find novel isoforms) or ... It aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bit/s reads per hour, which is ...
They determined that RIDGEs are very gene dense, have a high gene expression, short introns, high SINE repeat density and low ... Characteristics of ridges are: Gene dense Contain many C and G nucleobases Genes have short introns High SINE repeat density ... September 2003). "The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern ... Overlapping genes were treated as one gene, and genes without introns were rejected as pseudogenes. ...
... the terminus of the short arm, on chromosome 3. C3orf70 spans 74,964 bases containing two exons and two introns. The ...
In 96% of cases, the mutant FXN gene has 90-1,300 GAA trinucleotide repeat expansions in intron 1 of both alleles. This ... The length of the shorter GAA repeat is correlated with the age of onset and disease severity. The formation of heterochromatin ...
March 2009). "The effect of a short-term hypocaloric diet on liver gene expression and metabolic risk factors in obese women". ... The gene contains 3 exons and 4 distinct introns. The ISLR gene have two known transcript isoforms on the plus strands: ISLR ... Transcript variant 2 encodes for the shorter protein isoform with the length of 2,128 bp, containing 2 exons. This variant ... of ISLR in obese female human subjects demonstrated consistent low expression of ISLR in subjects that followed a short-term ...
It is shorter than variant 8 by one codon at the splicing junction between the first two exons. It is made by 153 aa. NCBI ... Telokin is transcribed from a second promoter, located within an intron, in the 3' region of the MLCK gene. And that is why the ... The first exon corresponds to intron 30 and there mainder of the transcript corresponds to the last two exons of the gene. ... The two transcrips that produce the two telokin isoforms are the following: Isoform 7 This variant encodes the shorter isoform ...
Organization and expression of immunoglobulin genes
These are a short leader (L) exon, a noncoding sequence (intron), a joined VJ segment, a second intron, and the constant region ... an intron, a joined VDJ segment, a second intron and several gene segments. The final product of the rearrangement is ... These reorganizations of gene segments produce gene sequence from 5 prime to 3 prime ends such as a short leader exon, ... The class switching involves switch regions that made up of multiple copies of short repeatts(GAGCT and TGGGG). These switches ...
2003, consists of about three exons separated by one short phase-2 (140 bp) and one long phase-1 (900 bp) intron. Exon 1 codes ... the protein is composed of a short N-terminal alpha helix, a type of protein formation, and a small antiparallel triple- ...
It was suggested that regulatory elements may be present within the first intron which is unusually large at more than 2.4 kb ... DmX has a relatively small promoter region that is likely shorter than 200 bp, leaving little space for regulatory elements. ...
The genome size for this microorganism is achieved by lack of, "pseudogenes, introns, transposons, extrachromosomal elements, ... Short JM, Carrington JC, Mathur EJ (August 2005). "Genome streamlining in a cosmopolitan oceanic bacterium". Science. 309 (5738 ... or inteins". The genome also contains fewer paralogs compared to other members of the same clade and the shortest intergenic ...
... or introns), which are short, non-coding regions that are found within genes, especially within the genes of eukaryotic ... Francis WR, Wörheide G (June 2017). "Similar Ratios of Introns to Intergenic Sequence across Animal Genomes". Genome Biology ...
... the average gene size is 1000 bp shorter in D. pulex. As inferred from expressed sequence tag analysis, the average intron size ... The intron density of the D. pulex genome, though, is similar to that of Apis mellifera, which in turn is twice that found in ... Such an efficient gene packaging is achieved by means of a small intron size. Indeed, whereas the mean protein length in D. ...
As in prokaryotes, genes in chloroplast DNA are organized into operons. Introns are common in chloroplast DNA molecules, ... Many chloroplast DNAs contain two inverted repeats, which separate a long single copy section (LSC) from a short single copy ... while they are rare in prokaryotic DNA molecules (plant mitochondrial DNAs commonly have introns, but not human mtDNA). ...
The female remains in the nest for almost all of the incubation period and is fed both by the male and during short breaks. ... de Kloet, RS; de Kloet SR (2005). "The evolution of the spindlin gene in birds: Sequence analysis of an intron of the spindlin ... have shorter lifespans up to 15-20 years. Some parrot species can be quite loud, and many of the larger parrots can be ... The lower mandible is shorter, with a sharp, upward-facing cutting edge, which moves against the flat portion of the upper ...
... s are believed to have evolved from ribosomal proteins with which they share much in common, both being short and basic ... In animals, genes encoding canonical histones are typically clustered along the chromosome, lack introns and use a stem loop ... Genes encoding histone variants are usually not clustered, have introns and their mRNAs are regulated with polyA tails. Complex ... the compacted molecule is 40,000 times shorter than an unpacked molecule. ...
分子演化 - 维基百科，自由的百科全书
... short interspersed nuclear element）和長散落元件（long interspersed nuclear element）。在靈長目中，最常見的短散落元件是Alu元件，長散落元件是CRISPR/Cas 系統
Arqueas, a enciclopedia libre
2002). "Introns in protein-coding genes in Archaea". FEBS Lett. 510 (1-2): 27-30. PMID 11755525. doi:10.1016/S0014-5793(01) ... Waters E; Hohn MJ; Ahel I; Lin X; Mathur E; Ni J; Podar M; Richardson T; Sutton GG; Simon M; Soll D; Stetter KO; Short JM; ... Waters E; Lin X; Mathur E; Ni J; Podar M; Richardson T; Sutton GG; Simon M; Soll D; Stetter KO; Short JM; Noordewier M (2003). ... Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA (1997). "Archaeal introns: splicing, intercellular mobility and ...
ವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯ
Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ (December 2012). "Introns in UTRs: why we should stop ignoring them.". ... Slack, J.M.W. Genes-A Very Short Introduction. Oxford University Press 2014 ...
The shortest was 165-bases long, though it has been estimated that only part of the molecule was crucial for this function. One ... of the RNA world than are introns or other RNAs then so considered. If so, viroids have attained potential significance ... The ability to catalyse the formation of peptide bonds between amino acids to produce short peptides or longer proteins. This ... The ability to catalyze one step in protein synthesis, aminoacylation of RNA, has been demonstrated in a short (five-nucleotide ...
Epigenetics of neurodegenerative diseases
ncRNA that is encoded antisense from an intron within the beta-amyloid cleaving enzyme gene, BACE1, is involved in AD. This ... The disease is characterized behaviorally by chronic and progressive decline in cognitive function, beginning with short term ... SMN2 are nearly identical except for a single nucleotide change in SMN2 resulting in an alternative splicing site where intron ...
Short, A K; Fennell, K A; Perreau, V M; Fox, A; O'Bryan, M K; Kim, J H; Bredy, T W; Pang, T Y; Hannan, A J (2016). "Elevated ... Shorter J, Lindquist S (June 2005). "Prions as adaptive conduits of memory and inheritance". Nature Reviews Genetics. 6 (6): ... good enough for short-term adaptation that allows the lineage to survive for long enough for mutation and/or recombination to ... subjects who carried one or two copies of the short allele of the serotonin transporter promoter polymorphism exhibited higher ...
... s live very short lives in captivity when compared to other cetaceans such as common bottlenose dolphins and short- ... "Phylogeny of the Beaked Whale Genus Mesoplodon (Ziphiidae: Cetacea) Revealed by Nuclear Introns: Implications for the ... 1.1 to 16.5 short tons). Their key distinguishing feature is the presence of a 'beak', somewhat similar to many dolphins. Other ...
Short tandem repeats are unique markers that can be used to determine haplotypes and are used in identity testing for maternal ... and small amounts of the flanking untranslated regions and introns are analyzed. Therefore, although these tests are highly ... Mendelian (single-gene) inheritance was studied in a number of important disorders such as albinism, brachydactyly (short ... short stature, and many others. Examples of genetic syndromes that are commonly seen in the genetics clinic include chromosomal ...
The other isoform (IL-15 SSP) has a short signal peptide of 21 amino acids encoded by exons 4A and 5. Both isoforms shared ... The human IL-15 gene comprises nine exons (1 - 8 and 4A) and eight introns, four of which (exons 5 through 8) code for the ... The other isoform (IL-15 SSP) has a short signal peptide of 21 amino acids encoded by exons 4A and 5. Both isoforms shared 11 ... and eight introns, four of which (exons 5 through 8) code for the mature protein (Figure 1). ...
The short-lived, unprocessed or partially processed product is termed precursor mRNA, or pre-mRNA; once completely processed, ... "Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes". PLoS ... In general, in prokaryotes the lifetime of mRNA is much shorter than in eukaryotes. Prokaryotes degrade messages by using a ... The editing creates an early stop codon, which, upon translation, produces a shorter protein. ...
Neurofilament light polypeptide
... a unique exon-intron organization in the intermediate filament gene family". Biochimica et Biophysica Acta. 909 (1): 10-20. doi ... is located on the short arm of chromosome 8". Cytogenetics and Cell Genetics. 45 (1): 30-2. doi:10.1159/000132421. PMID 3036423 ...
Mobile genetic elements - Simple English Wikipedia, the free encyclopedia
This short article about biology can be made longer. You can help Wikipedia by adding to it. ... Group II introns. The total of all mobile genetic elements in a genome may be referred to as the mobilome. ...
Higher fertility rates and shorter or less parental care per child is another association that may be a compensation for the ... brand names Pegasys or PEG-Intron) combined with ribavirin, it has been shown that genetic polymorphisms near the human IL28B ... The unusual texture of the bone around the wounds suggests they were afflicted by a short-lived, non-lethal infection. ... providers should treat an infection with an antimicrobial that specifically works well for the target pathogen for the shortest ...
Short radio episode Baseball from "Lil' Yokohama" by Toshio Mori, 1941. California Legacy Project. ... There is a very common pattern of two different cholesterol ester transfer protein gene mutations (D442G, 5.1%; intron 14G:A, ... Apolo Anton Ohno (hapa) won eight Olympic medals in short-track speed skating (two gold) in 2002, 2006, and 2010, as well as a ... Chris Tashima won the Academy Award for Best Live Action Short Film in 1997. ...
In a study that used mitochondrial and nuclear intron DNA, the black-throated loon was found to be sister to a clade consisting ... The lower throat has a necklace-shaped patch of short parallel white lines. The sides of the throat have about five long ... Most dives, about 80% of them, are successful, and those that are successful are usually shorter than those that are ... whereas a study using mitochondrial and nuclear intron DNA supported placing the black-throated loon sister to a clade ...
Peppered moth evolution
The region that was used to find it was the first intron of the orthologue of the cortex gene in Drosophila. Through ... Articles with short description. *Short description matches Wikidata. *Use dmy dates from September 2012 ...
Mir-181 microRNA precursor
Tang GQ, Maxwell ES (January 2008). "Xenopus microRNA genes are predominantly located within introns and are differentially ... short-tailed opossum (Monodelphis domestica), rhesus macaque (Macaca mulatta), mouse (Mus musculus), pig-tailed macaque (Macaca ...
Comparative analysis of a translocated copy of the trnK intron in carnivorous family Nepenthaceae. Molecular Phylogenetics and ... Inflorescences have a very dense indumentum of short, white or brownish stellate hairs. The pedicels, tepals and the ovary are ... Molecular phylogeny of Nepenthaceae based on cladistic analysis of plastid trnK intron sequence data. Plant Biology 3(2): 164- ...
At the carboxyl terminal of the peptide chain there's a short alpha helix domain that allows tetramerization. The central ~ ... "Association of DNA polymorphism in the first intron of the tyrosine hydroxylase gene with disturbances of the catecholaminergic ... Tyrosine hydroxylase activity is increased in the short term by phosphorylation. The regulatory domain of tyrosine hydroxylase ...
Open reading frame
ORFs span intron/exon regions, which may be spliced together after transcription of the ORF to yield the final mRNA for protein ... it has been proven that some short ORFs (sORFs) that lack the classical hallmarks of protein-coding genes (both from ncRNAs and ...
The tail is the shortest of any big cat, at 45 to 75 cm (18 to 30 in) in length. Legs are also short, but thick and ... with novel application of nuclear beta-fibrinogen intron 7 to carnivores". Molecular Phylogenetics and Evolution. 35 (2): 483- ... A short and stocky limb structure makes the jaguar adept at climbing, crawling, and swimming. The head is robust and the ... powerful, considerably shorter when compared to a small tiger or lion in a similar weight range. The jaguar stands 63 to 76 cm ...
Steven Okazaki won the 1990 Academy Award for Best Documentary (Short Subject) for his film Days of Waiting: The Life & Art of ... There is a very common pattern of two different cholesterol ester transfer protein gene mutations (D442G, 5.1%; intron 14G:A, ... Short radio episode Baseball from "Lil' Yokohama" by Toshio Mori, 1941. California Legacy Project. ... Chris Tashima won the 1997 Academy Award for Best Live Action Short Film. Audrey Marrs won the 2010 Academy Award for Best ...
Phillip Allen Sharp
"Short Bio - Phillip A. Sharp". Sharp Lab. Retrieved 12 November 2014.. *^ Biogen Idec, Inc. (2008). "Proxy statement for annual ... "the discovery that genes in eukaryotes are not contiguous strings but contain introns, and that the splicing of messenger RNA ... Petersen C.P.; Bordeleau M.E.; Pelletier J.; Sharp P.A. (17 February 2006). "Short RNAs Repress Translation after Initiation in ... to delete those introns can occur in different ways, yielding different proteins from the same DNA sequence". ...
Some pre-tRNAs contain introns that are spliced, or cut, to form the functional tRNA molecule; in bacteria these self- ... tRNA-derived fragments (or tRFs) are short molecules that emerge after cleavage of the mature tRNAs or the precursor transcript ... ends of the spliced intron sequence. The 5' sequence is removed by RNase P, whereas the 3' end is removed by the tRNase ... including the relatively long tRNA halves and short 5'-tRFs, 3'-tRFs and i-tRFs. The precursor tRNA can be cleaved ...
5-HT is short for 5-hydroxy-tryptamine, which is serotonin. This is the main excitatory receptor subtype among the GPCRs for ... across 68 genes were investigated and a SNP-termed rs7997012-in the second intron of the HTR2A gene showed significant ...
Granulocyte colony-stimulating factor
found that the GCSF gene has 4 introns, and that 2 different polypeptides are synthesized from the same gene by differential ... McCracken S, Layton JE, Shorter SC, Starkey PM, Barlow DH, Mardon HJ (May 1996). "Expression of granulocyte-colony stimulating ...
N-lobe corresponds to amino acid residues 1-333 and C-lobe to 345-692, and the ends of those domains are connected by a short α ... whereas the sizes of introns differ within the family. Similarity in the size of exons and their distribution in the domains of ...
Selection for short introns in highly expressed genes. - PubMed - NCBI
Selection for short introns in highly expressed genes.. Castillo-Davis CI1, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. ... This difference is greater in humans, such that introns are, on average, 14 times shorter in highly expressed genes than in ... Thus, natural selection appears to favor short introns in highly expressed genes to minimize the cost of transcription and ... we show that introns in highly expressed genes are substantially shorter than those in genes that are expressed at low levels. ...
Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro. | Molecular and...
Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro.. A Mayeda, Y Ohshima ... Thus, a short sequence inserted within an intron can be an active donor site signal in the presence of an authentic donor site ... Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro. ... Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro. ...
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes | BMC Evolutionary Biology |...
The short introns in highly expressed genes should not be attributed to energy constraint. We evaluated evidence for the time ... According to the energetic cost hypothesis, the former should have shorter introns than the latter. However, in humans and mice ... highly expressed genes have shorter introns than weakly expressed genes. A popular explanation for this is selection for ... Qualitative estimation shows that the deleterious effect (that is, the energetic burden) of long introns in highly expressed ...
Classification of Short Human Exons and Introns based on Statistical Features
If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of ... The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this ... which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that ...
Microsatellite - Wikipedia
Effects within introns. Microsatellites within introns also influence phenotype, through means that are not currently ... Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy, or as ... Weber J.L., Wong C. (1993). "Mutation of human short tandem repeats". Hum. Mol. Genet. 2 (8): 1123-1128. doi:10.1093/hmg/2.8. ... Scherer S. (2008). A short guide to the human genome. New York: Cold Spring Harbor University Press.. ...
Identification and validation of evolutionarily conserved unusually short pre-mRNA introns in the human genome<...
Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the ... Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the ... Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the ... Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the ...
Identification of Short Exons Disunited by a Short Intron in Eukaryotic DNA Regions - BioTech Mag
Weak codon bias in short exons and separation by a short intron induces difficulty in extracting period-3 component that marks ... Identification of Short Exons Disunited by a Short Intron in Eukaryotic DNA Regions 13 days ago - By IEEE/ACM ... Weak codon bias in short exons and separation by a short intron induces difficulty in extracting period-3 component that marks ... period-3 spectrums corresponding to multiple mappings have been optimized to enhance short exon-short intron discrimination, ...
A primate subfamily of galectins expressed at the maternal-fetal interface that promote immune cell death | PNAS
Numbers indicate chromosomal locations; short arrows show coding strand orientations. Positions of genes (introns, yellow; ... 3 shows that short interspersed transposable elements (SINEs) are the most frequent repetitive transposable elements directly ... resulting in relatively short gestations and small offspring (5). As an alternative reproductive strategy, anthropoids retained ... mutations of the exon-intron boundaries, and the introduction of 1 or more in-frame premature stop codons. Strikingly, 18 ...
Both Size and GC-Content of Minimal Introns Are Selected in Human Populations
... tend to have a higher ratio of deletion to insertion than those that are shorter than the optimal size; (ii) GC-effect: minimal ... 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 ...
A functional role for some Fugu introns larger than the typical short ones: The example of the gene coding for ribosomal...
Although short, the six introns are longer than the ~100 bp size of most Fugu introns, as they host U17 RNA coding sequences. ... Although short, the six introns are longer than the ~100 bp size of most Fugu introns, as they host U17 RNA coding sequences. ... Although short, the six introns are longer than the ~100 bp size of most Fugu introns, as they host U17 RNA coding sequences. ... Although short, the six introns are longer than the ~100 bp size of most Fugu introns, as they host U17 RNA coding sequences. ...
Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich...
Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich ... we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1. gene, the 49-nt intron in the NDOR1. (NADPH ... SF3b (U2 snRNP component) is involved in splicing of these 3 ultra-short introns. Splicing of the 56-nt intron requires the U1 ... The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 ...
Many P-Element Insertions Affect Wing Shape in Drosophila melanogaster | Genetics
Exons are thick; introns are thin. The diagrams do not show some very short introns. Gene symbols are given according to ... Two are long and include a 17-kb central intron, and the other two are short and start inside this central intron, beginning ... Insertions may fall in a short interval between two genes or in an intron containing other genes. In some cases the gene ... The insertion site is in the first intron of the gene sugarless (sgl). The intron is ∼2.4 kb long, and the insertion is at the ...
'Junk' DNA: evolutionary discards or God's tools? - creation...
The presence of introns throughout genes allows the proper levels to be maintained, and indeed introns reflect the general ... Izsvak, Z., Ivics, Z., Shimoda, N., Mohn, D., Okamoto, H. and Hackett, P.B., Short inverted-repeat transposable elements in ... Another observed mechanism by which introns can regulate gene activity is through the binding of the snipped-out intron RNA to ... Another example of selective interpretation of DNA sequence comparison data using introns is the study of an intron in an ...
Intron - Wikipedia
... end of the intron during the splicing process, generating a branched (lariat) intron. Apart from these three short conserved ... 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 ...
Growth hormone insensitivity and severe short stature in siblings: A novel mutation at the exon 13-intron 13 junction of the...
Growth hormone insensitivity and severe short stature in siblings: A novel mutation at the exon 13-intron 13 junction of the ... Growth hormone insensitivity and severe short stature in siblings: A novel mutation at the exon 13-intron 13 junction of the ... Growth hormone insensitivity and severe short stature in siblings : A novel mutation at the exon 13-intron 13 junction of the ... T1 - Growth hormone insensitivity and severe short stature in siblings. T2 - A novel mutation at the exon 13-intron 13 junction ...
Release Notes for Genome Workbench 3.0.1 (August 20, 2019)
Graphical Sequence View: fixed issues with rendering of short introns. *Graphical Sequence View: improved consistency of visual ... to correctly account for introns (graphics now include intron row) ... Alignment Span View: fixed issue with incorrect Exon/Intron boundaries for amino acids encoded across a splice junction shown ... Graphical Sequence View: fixed issue showing some extra amino acid in ProSplign alignment in intron part ...
Pediatric Thalassemia: Practice Essentials, Background, Pathophysiology
Both exons and introns are initially present on this mRNA precursor; the introns are ultimately subsequently eliminated, and ... Each of these regulatory sequences has a modular structure that consists of short nucleotide motifs that act as binding sites ... Both ends of the RNA introns (at the junction with the exons) have specific consensus sequences; these motifs include GT in the ... These mutations occur in both exons and introns. For example, in a nonsense mutation, a single base change in the exon ...
Basic molecular genetics for epidemiologists | Journal of Epidemiology & Community Health
INTRON. Each of the segments of a gene that are not transcribed into messenger RNA and that are found between exons. ... MICROSATELLITE (SYNOMYN, SHORT TANDEM REPEAT, STR). DNA segment consisting in the repetition 5-50 times of a motif 1-6 ... Obviously, the topics are so extensive and innovative that a single short glossary would not be sufficient to provide you with ... Hence, we have organised the manuscript in three short glossaries that will try to guide you from the most basic molecular ...
Intron - Wikipedia
... end of the intron during the splicing process, generating a branched (lariat) intron. Apart from these three short conserved ... 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 ( ...
Frontiers | Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred | Genetics
Hubé, F., Ulveling, D., Sureau, A., Forveille, S., and Francastel, C. (2017). Short intron-derived ncRNAs. Nucleic Acids Res. ... Kageyama, Y., Kondo, T., and Hashimoto, Y. (2011). Coding vs non-coding: translatability of short ORFs found in putative non- ... Xu, Q., Walker, D., Bernardo, A., Brodbeck, J., Balestra, M. E., and Huang, Y. (2008). Intron-3 retention/splicing controls ... 2006). Alternative splicing of the first intron of the steroid receptor RNA activator (SRA) participates in the generation of ...
tRNA-splicing endonuclease subunit Sen15 (IPR018593) | InterPro | EMBL-EBI
"Junk DNA" Suffers a Blow as Nature Papers Find "Global Function" for Introns in Budding Yeast | Evolution...
Most of these introns are shorter than 500 nucleotides in length and only nine yeast genes possess more than one intron ( ... 10b, c). Together, the data present a paradigm of intron function in which the presence of introns directly contributes to cell ... Lower eukaryotes (for example, yeast) tend to have shorter and fewer introns. While they were once thought to be junk - genetic ... Introns are segments of genes, found in eukaryotes, that do not code for proteins. Introns are removed from the pre-mRNA ...
Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA.
... the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. ... but scattered distribution of group I introns in nature is a result of two processes; ... During the process, the short internal guide sequence (IGS; 4-6 nt) near the 5′ end of the free intron RNA recognizes the ... In this manner, the biological role of intron FLCs would be intron horizontal transfer mediated by intron integration at the ...
Splicing heterogeneity: separating signal from noise | SpringerLink
A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A. 2001;98:11193 ... even for short introns (≤ 134 bp) in human transcripts . Moreover, many sequences in the mammalian genome match the ... then assemble to complete intron removal and exon ligation, and then disassemble. Intron and exon definition is the key step in ... The 5′ splice site consensus AG,GURAGU is present at the exon-intron junction. The 15-nucleotide 3′ splice site Y10NCAG,G is ...
Workshop on The Long and The Short of it: Role of ncRNAs in Hematopoiesis | NIDDK
Intron Retention and Its Role in Granulopoiesis. Justin Wong, University of Sydney. 2:10 p.m.. Composition of the ncRNA "Milieu ... Workshop on The Long and The Short of it: Role of ncRNAs in Hematopoiesis. Aug. 30, 2013. Contacts ... Workshop on The Long and The Short of it: Role of ncRNAs in Hematopoiesis ...
SEN1 - tRNA-splicing endonuclease subunit Sen2-1 - Arabidopsis thaliana (Mouse-ear cress) - SEN1 gene & protein
There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, ... The products are an intron and two tRNA half-molecules bearing 2,3-cyclic phosphate and 5-OH termini. ... It cleaves pre-tRNA at the 5- and 3-splice sites to release the intron. ... IPR036167. tRNA_intron_Endo_cat-like_sf. IPR006677. tRNA_intron_Endonuc_cat-like. IPR006678. tRNA_intron_Endonuc_N. IPR006676. ...
BZIP intron RNA motif - Wikipedia
The consensus intron is very short in Metazoa (20, 23 or 26 nt). However, yeast species have a long (>100 nt) intron in HAC1. ... The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 ... Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/ ... intron boundaries. Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). The Ire- ...
Deubiquitinase USP47-stabilized splicing factor IK regulates the splicing of ATM pre-mRNA | Cell Death Discovery
Intron 1 in the ATM pre-mRNA, having lengths ,200 bp, was not spliced in the IK-depleted cells and led to a deficiency of the ... 3a). Because previous report showed IK was related in splicing of short intron8, we also checked the intron sizes in ATM pre- ... Although ATM has many introns, only intron 1 was not spliced in absence of IK because it has a short length. This result ... 8 reported that IK and SMU1 play a critical role in the excision of short introns. In other words, introns retained after the ...
Supplementary Material for: An Intron 9 CYP19 Gene Variant (IVS9+5G|A), Present in an Aromatase-Deficient Girl, Affects Normal...
An Intron 9 CYP19 Gene Variant (IVS9+5G,A), Present in an Aromatase-Deficient Girl, Affects Normal Splicing and Is Also Present ... Protein analysis showed a shorter and inactive protein. The intron 9 transcript variant was also found in human steroidogenic ... b,,i,Conclusions:,/i,,/b, The mutation IVS9+5G,A generates a splicing variant that includes intron 9 which is also present in ... Supplementary Material for: An Intron 9 CYP19 Gene Variant (IVS9+5G,A), Present in an Aromatase-Deficient Girl, Affects Normal ...
Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA | eLife
... also has a very short half-life and can be rate limiting. We found a wide variation of minor intron dependence on U6atac level ... Gene structures are depicted in blue boxes (exons) and lines (introns). (E) Same as in (D) for low efficiency minor intron. (F ... Splicing of minor introns, typically one amidst several major introns, is dependent on the limiting level of U6atac snRNP in ... U12 intron positions are more strongly conserved between animals and plants than U2 intron positions * MK Basu ...
Expressed genesSequencesSequenceSplice sitesExon and intronMRNAGenomeNucleotidesRepeat polymorphism in intron1977TranscriptInclude intronGroup I intrSpecific intronHigher GC contentExons and intronsSegments of genesLariatProteinSaccharomycesLong intronsSingle intronYeastDrosophilaSpliceosomesEukaryotesUbiquitousHighly conservedLarge genomesOrganismsIntronicPolymorphismSpeciesBoundariesEukaryotic genomesPolypyrimidine tractMoleculesGenomesLengthsEvolutionaryTranscriptsEncodesMitochondrialTypicallyAbstractMutationHomologousOccur2019ProteinsLengthGene expressionRecombinationDonorSelectiveDistinctRemovalDeletionTranscriptionSplicingSpliceosomalInterruptionsAdjacent exonsGenomicAlleleLacksDensityHuman genesJunkMicroRNAs
- Selection for short introns in highly expressed genes. (nih.gov)
- Thus, at least for highly expressed genes, transcription of long introns, which are particularly common in mammals, is costly. (nih.gov)
- 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)
- This difference is greater in humans, such that introns are, on average, 14 times shorter in highly expressed genes than in genes with low expression, whereas in C. elegans the difference in intron length is only twofold. (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)
- Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro. (asm.org)
- We constructed SP6-human beta-globin derivative plasmids that included possible donor site (5' splice site) sequences at a specified position within the first intron. (asm.org)
- The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. (edu.au)
- 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. (edu.au)
- By conducting BLAST searches of the databases, we screened 22 introns (37-65 nt) with conserved lengths and sequences among closely related species. (fujita-hu.ac.jp)
- The annotation task of such short exons has been addressed in the proposed model independent signal processing based method with following features: DNA sequences have been mapped using multiple mapping schemes, period-3 spectrums corresponding to multiple mappings have been optimized to enhance short exon-short intron discrimination, and spectrums corresponding to multiple mapping schemes have been subjected to Principal Component. (biotechmag.top)
- 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. (elsevier.com)
- Although short, the six introns are longer than the ~100 bp size of most Fugu introns, as they host U17 RNA coding sequences. (elsevier.com)
- Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers. (geoscience.net)
- 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)
- Nuclear pre-mRNA introns (spliceosomal introns) are characterized by specific intron sequences located at the boundaries between introns and exons. (wikipedia.org)
- Apart from these three short conserved elements, nuclear pre-mRNA intron sequences are highly variable. (wikipedia.org)
- There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. (uniprot.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)
- Accumulation of this splicing intermediate and use of an innovative reverse transcriptase-polymerase chain reaction technique (J. Vogel, R.H. Wolfgang, T. Borner  Nucleic Acids Res 25: 2030-2031) led to the identification of 3′ intron sequences needed for lariat formation. (plantphysiol.org)
- Some conserved but short terminal sequences within introns function in intron splicing. (plantphysiol.org)
- One possibility is, "Introns originated to circumvent the problem of the random distribution of stop codons in random primordial sequences" (6) . (panspermia.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)
- Recent studies have produced data that shed light on the pattern of intron properties, e.g., the variations of length, GC content, ordinal position in a gene (first intron, second intron, and so on) and divergence of intron sequences. (biomedcentral.com)
- There are few non-coding sequences, called introns. (sciencelearn.org.nz)
- 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)
- F. Gao and C. T. Zhang, (2004) Comparison of various algo-rithms for recognizing short coding sequences of human genes, Bioinformatics, 20, 673-681. (scirp.org)
- Thus, a short sequence inserted within an intron can be an active donor site signal in the presence of an authentic donor site. (asm.org)
- Microsatellites are often referred to as short tandem repeats ( STRs ) by forensic geneticists and in genetic genealogy , or as simple sequence repeats ( SSRs ) by plant geneticists. (wikipedia.org)
- Fifth, intron GC content and sequence divergence tend to have an adverse correlation  . (plos.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)
- 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)
- The sequence of the intron is well conserved only around the splice sites. (wikipedia.org)
- Prominent clinical findings included short stature with platyspondyly, flat midface and Pierre Robin sequence, severe dysplasia of the proximal femora, and severe retinopathy that could lead to blindness. (springer.com)
- DNA sequence analysis of the bt2 - 7503 mutant allele of the maize brittle-2 gene revealed a point mutation in the 5′ terminal sequence of intron 3 changing GT to AT. (plantphysiol.org)
- Although introns are ubiquitous and share a high degree of structural/sequence similarity across species, the signals that specifically define splice sites are not completely understood. (plantphysiol.org)
- In yeast, introns possess a highly conserved branch point sequence UACUAAC 10 to 50 nt upstream of the 3′ splice site. (plantphysiol.org)
- Particular structural and sequence features distinguish plant introns from those of vertebrates and yeast. (plantphysiol.org)
- A computational analysis of sequence features involved in recognition of short introns. (mit.edu)
- Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. (mit.edu)
- We present a novel approach, called QPALMA , for computing accurate spliced alignments of short sequence reads that take advantage of the read's quality information as well as computational splice site predictions. (biomedcentral.com)
- 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)
- 8. The method of claim 7 , wherein said sequenced provirus is compared to said genomic DNA sequence to determine exon and intron boundaries. (google.com)
- Our data indicate that gene function, expression level, and sequence conservation influence TE insertion/fixation in mammalian introns. (biomedcentral.com)
- 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)
- Key to this process are short sequence motifs. (evolutionnews.org)
- The first transesterification reaction then takes place, and a cut is made at the 5′ splice site and the 5′ end of the intron is subsequently connected to the conserved adenine found in the branch point sequence, forming the so-called "lariat" structure. (evolutionnews.org)
- We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. (fujita-hu.ac.jp)
- Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/intron boundaries. (wikipedia.org)
- The secondary structure of the bZIP intron is very well conserved, and consists of two hairpins (H2 and H3) around the splice sites, and an extended hairpin (H1) that brings the splice sites together (see figure). (wikipedia.org)
- It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. (uniprot.org)
- In an attempt to address the functionality issue, we considered separately major (mostly included) and minor (mostly skipped) cassette exons, alternative splice sites corresponding to shorter or longer exon variants (internal and external alternative splice sites, respectively), and frame-preserving or frame-shifting alternatives. (biomedcentral.com)
- 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)
- The first stage in RNA splicing is recognition by the spliceosome of splice sites between introns and exons. (evolutionnews.org)
Exon and intron2
- 0.001 in most cases): an ordinal reduction of length and divergence in both exon and intron, a co-variation between exon and its flanking introns in their length, GC content and divergence, and a decrease of average exon (or intron) length, GC content and divergence as the total exon numbers of a gene increased. (biomedcentral.com)
- hnRNA products transcribed off the DNA template strand include exon and intron equivlaents . (mun.ca)
- Shimada, MK , Sasaki-Haraguchi, N & Mayeda, A 2015, ' Identification and validation of evolutionarily conserved unusually short pre-mRNA introns in the human genome ', International journal of molecular sciences , vol. 16, no. 5, pp. 10376-10388. (fujita-hu.ac.jp)
- Nuclear pre-mRNA introns are often much longer than their surrounding exons. (wikipedia.org)
- Simple illustration of an unspliced mRNA precursor, with two introns and three exons (top). (wikipedia.org)
- In Saccharomyces cerevisiae the long intron pairs with the 5′ UTR and stalls the ribosomes on the mRNA. (wikipedia.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)
- 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)
- Hac1p is only produced when an intron at the 3' end of its mRNA is removed by a nonconventional, regulated splicing reaction. (semanticscholar.org)
- We show that a previously unrecognized base-pairing interaction between the intron and the 5' untranslated region is required and sufficient to block mRNA translation. (semanticscholar.org)
- Usually, the mRNA copy is a bit shorter than its DNA precursor. (mskcc.org)
- If the mRNA copy doesn't include all of the exons in a gene or is cut short, then the protein made from that mRNA will also be truncated. (mskcc.org)
- Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. (blogspot.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 animation above reveals this astonishing machine at work on the precursor mRNA, cutting out the non-coding introns and splicing together the protein-coding exons. (evolutionnews.org)
- Introns (which, unlike exons, do not code for proteins) can be of considerable length in higher eukaryotes, even spanning many thousands of bases and sometimes comprising some 90% of the precursor mRNA. (evolutionnews.org)
- Since introns are the non-coding segments of genes, they are removed from the mRNA before it is translated into a protein. (evolutionnews.org)
- There are also ATPases that promote the structural rearrangements of snRNAs and release by the spliceosome of mRNA and the intron lariat. (evolutionnews.org)
- Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. (fujita-hu.ac.jp)
- 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)
- The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. (elsevier.com)
- 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)
- 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)
- 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)
- 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)
- In a typical application scenario one needs to align millions of short reads against the genome. (biomedcentral.com)
- We were able to successfully exploit all available information sources - the read including its quality score information, splice site predictions, the intron length and, of course, the genome - each significantly contributing to decreasing the alignment error rate. (biomedcentral.com)
- AsDTS7 transcript contains 1024 bp that is interrupted in the genome by 3 short introns ranging in size from 57-66 nts. (usda.gov)
- Through follow-up DNA sequencing and computational analyses, the researchers determined the dogs' disproportionately short limbs can be traced to one mutational event in the canine genome - a DNA insertion - that occurred early in the evolution of domestic dogs. (genome.gov)
- These included 3 to 8 nucleotides of an exon and 6 to 8 nucleotides of an intron. (asm.org)
- According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. (fujita-hu.ac.jp)
- 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)
Repeat polymorphism in intron2
- Previous studies have demonstrated a dinucleotide (CA) n repeat polymorphism in intron 1 of EGFR , ranging from 14 to 21 repeats, that has been suggested to regulate EGFR expression. (aacrjournals.org)
- In the present study, we investigated the relationship between an important 27 bp repeat polymorphism in intron 4 of eNOS and numbers of circulating EPCs in presence of cardiovascular disease (CVD) risk factors in a group of healthy human volunteers. (springer.com)
- 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)
- Introns were first identified in 1977 by the lab of Richard Roberts and Phil Sharp (Chow et al . (evolutionnews.org)
- A surprising phenomenon was discovered in 1977 - introns. (panspermia.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)
- 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)
- The intron 9 transcript variant was also found in human steroidogenic tissues. (figshare.com)
- The accurate removal of introns from the primary transcript is a fundamental process essential for the expression of eukaryotic genes. (plantphysiol.org)
- The graphic also shows two versions of short and long transcript variants produced, along with areas of transcription factor binding. (icr.org)
- Most mature transcripts include intron 3, while the second most frequent class lacks exon 3. (plantphysiol.org)
Group I intr4
- Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA. (biomedsearch.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)
- 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)
- 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)
- 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)
Higher GC content3
- ii) GC-effect: minimal introns with lower GC content tend to be more frequently deleted than those with higher GC content. (plos.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)
- 18 ] found that the class of long introns had higher GC content and lower divergence than that of short introns in fruit fly. (biomedcentral.com)
Exons and introns4
- 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. (edu.au)
- However, there is little study about the structural variation of exons and introns. (biomedcentral.com)
- We investigated the length, GC content, ordinal position and divergence in both exons and introns of 13 eukaryotic genomes, representing plant and animal. (biomedcentral.com)
- Therefore, a systematic investigation of the properties of both exons and introns will provide a framework for understanding the mechanisms determining exon-intron architecture. (biomedcentral.com)
Segments of genes1
- Introns are segments of genes, found in eukaryotes, that do not code for proteins. (evolutionnews.org)
- The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. (geoscience.net)
- In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. (geoscience.net)
- The second step involves cleavage at the 3′ intron splice site, release of the intron lariat, and ligation of the two adjacent exons. (plantphysiol.org)
- By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. (geoscience.net)
- 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)
- Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). (wikipedia.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)
- Protein analysis showed a shorter and inactive protein. (figshare.com)
- As far as we know, this truncating mutation in the C-propeptide region is the farthest one from the 3' end of the gene that causes a disease with short stature, suggesting the existence of the mutant protein. (springer.com)
- 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)
- Specifically, they are located in areas of genes called introns, short stretches of DNA that are not involved in making a protein. (eurekalert.org)
- Specifically, the researchers found that in contrast to other dog breeds, all short-legged dog breeds have an extra copy of the gene that codes for a growth-promoting protein called fibroblast growth factor 4 (FGF4). (genome.gov)
- In the case of short-legged dogs, the inserted retrogene results in the overproduction of the FGF4 protein, which researchers hypothesize may turn on key growth receptors at the wrong times during fetal development. (genome.gov)
- The spliceosome catalyzes a reaction that results in intron removal and the "gluing" together of the protein-coding exons. (evolutionnews.org)
- 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)
- 2016). Identification of new branch points and unconventional introns in saccharomyces cerevisiae. (mit.edu)
- In addition, we observed that the shorter introns had either low or high GC content, and the GC content of long introns was intermediate. (biomedcentral.com)
- The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 in yeast, XBP1 in Metazoa, Hxl1 or Cib1 in Basidiomycota and bZIP60 in plants. (wikipedia.org)
- However, yeast species have a long (>100 nt) intron in HAC1. (wikipedia.org)
- Lower eukaryotes (for example, yeast) tend to have shorter and fewer introns. (evolutionnews.org)
- The latest issue of Nature carries a paper on the functions of introns in budding yeast (Parenteau et al . (evolutionnews.org)
- A systematic deletion set of all known introns in budding yeast genes indicates that, in most cases, cells with an intron deletion are impaired when nutrients are depleted . (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)
- Several labs have looked closely at the small number of essential introns in yeast and determined that some of them are essential because they contain other genes, such as snoRNA genes. (blogspot.com)
- 2019) [ Yeast loses its introns ]. (blogspot.com)
- The bottom line, as far as I'm concerned, is that something like 99.7% of all the introns in the ancestor of modern Baker's yeast were junk but there's a small number that have secondarily acquired a function. (blogspot.com)
- Here, we review possible new mechanisms of intron functions, with a focus on the role of yeast introns in regulating the cell growth response to starvation. (blogspot.com)
- In contrast, lower eukaryotes such as yeast possess fewer and shorter introns, which are typically fewer than 300 bases in length. (evolutionnews.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)
- A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 megabase (Mb) intron, which takes roughly three days to transcribe. (wikipedia.org)
- Introns are ubiquitous features of all eukaryotic cells. (evolutionnews.org)
- Introns are ubiquitous in eukaryotic transcripts. (blogspot.com)
- Clearly, removing introns correctly from pre-mRNAs is important but cannot explain their ubiquitous preservation in genomic DNA across the course of evolution. (blogspot.com)
- Minor introns occur in many highly conserved genes, but they are often inefficiently spliced. (elifesciences.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)
- 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)
- Introns are now known to occur within a wide variety of genes throughout organisms and viruses within all of the biological kingdoms. (wikipedia.org)
- The frequency of introns within different genomes is observed to vary widely across the spectrum of biological organisms. (wikipedia.org)
- However, introns are also preserved in organisms where alternative splicing and splicing-dependent regulation of gene expression are rare. (blogspot.com)
- Splicing of the 49- and 43-nt introns requires G-rich intronic splicing enhancers. (geoscience.net)
- We previously have studied the insertion and deletion polymorphism by sequencing no more than one hundred introns in a mixed human population and found that the minimal introns tended to maintain length at an optimal size. (plos.org)
- Major interethnic differences in the allelic frequencies of the EGFR intron 1 polymorphism exist. (aacrjournals.org)
- The study suggests that the presence of CVD risk factors in subjects with eNOS intron 4 polymorphism results in reduced number of circulating EPCs, which may significantly predispose them to CVD and aberrant endothelial repair. (springer.com)
- Matyar S, Attila G, Akpinar O, Inal T. eNOS gene intron 4 a/b VNTR polymorphism is a risk factor for coronary artery disease in Southern Turkey. (springer.com)
- Computational methods predict a bZIP intron with its characteristic RNA structure in 128 out of 156 species studied. (wikipedia.org)
- In Fungi a bZIP intron was initially found only in Ascomycota (in 52 out of 63 species analysed) but experimental studies showed it is also present in Basidiomycota and other Candida species. (wikipedia.org)
- the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. (biomedsearch.com)
- 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)
- 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)
- 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)
- In addition to what it reveals about short-legged dogs, the unexpected discovery provides new clues about how physical differences may arise within species and suggests new approaches to understanding a form of human dwarfism. (genome.gov)
- Here, we provide revised gene models for D . ananassae , D. yakuba , and D. simulans , which include untranslated regions and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. (g3journal.org)
- We have presented a novel approach to solve the difficult task of aligning short reads as generated by NG sequencing techniques over exon boundaries. (biomedcentral.com)
- We compute the fraction of reads that have been accurately aligned at all four boundaries (start and end of first and second exon) with and without using read quality information, splice site predictions and intron length scoring, respectively. (biomedcentral.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)
- These clues provide a framework for elucidating mechanisms involved in the organization of eukaryotic genomes and particularly in building exon-intron structures. (biomedcentral.com)
- In addition, vertebrate introns possess a unique, 10- to 15-nt polypyrimidine tract located near the 3′ end that interacts with splicing factor U2AF during early spliceosome assembly. (plantphysiol.org)
- Splicing of all intron-containing RNA molecules is superficially similar, as described above. (wikipedia.org)
- 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)
- The products are an intron and two tRNA half-molecules bearing 2',3'-cyclic phosphate and 5'-OH termini. (uniprot.org)
- c) Mirtrons are located within introns and exploit the splicing machinery to generate functional miRNA molecules. (els.net)
- In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. (wikipedia.org)
- 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)
- Last, adaptive and purifying selection can work together to keep the lengths of short introns around an optimum size  . (plos.org)
- 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)
- 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  . (plos.org)
- Traditionally, the former class of transcripts is taken as evidence for the intron definition of splicing, while the latter class has given credence to the exon definition of splicing. (plantphysiol.org)
- We have identified a nuclear gene ( OTP43 ) absolutely required for trans -splicing of intron 1 (and only intron 1) of Arabidopsis thaliana nad1 transcripts. (plantcell.org)
- It encodes isoform b which has a shorter and distinct C-terminus compared to isoform a. (genome.jp)
- 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)
- Typically, when all trees within 1% of the shortest tree are combined into a consensus tree, there is little structure left. (grisda.org)
- abstract = "Background/Aims: Growth hormone insensitivity (GHI) is characterized by severe short stature, high serum growth hormone (GH), low serum IGF-I and IGFBP-3 levels and is classically associated with genetic defects of the GH receptor (GHR). (elsevier.com)
- If you would like to be considered but have not yet applied, please submit your application with an abstract or short description of your work as soon as possible. (bio.net)
- Of all the reported truncating mutations in the C-propeptide region that result in short-stature type II collagenopathies, this mutation is the farthest from the C-terminal of COL2A1 . (springer.com)
- i.e. introns can insert themselves into the homologous site in an intron-less allele (intron homing), or less frequently, they may spread into a new site in the same or a different gene. (biomedsearch.com)
- 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)
- A generates a splicing variant that includes intron 9 which is also present in normal human steroidogenic tissues, suggesting that a misbalance between normal and aberrant splicing variants might occur in target tissues, explaining the clinical phenotype in the affected patient. (figshare.com)
- The breaks between them, the introns, sometimes occur in the middle of a domain (5) . (panspermia.org)
- Parenteau, J., and Elela, S. A. (2019) Introns: Good Day Junk Is Bad Day Treasure. (blogspot.com)
- 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)
- Introns need to be removed from nascent messenger RNA through the process of splicing to produce functional proteins. (evolutionnews.org)
- The action of Drosha and DGCR8 proteins initiates the miRNA maturation producing shorter pre‐miRNA molecule. (els.net)
- We also discovered an effect that the length of minimal introns tended to be maintained at an optimal size based on re-sequencing 93 representative minimal introns and 12 indels in an average of 45.7 random samples from a world-wide human population  . (plos.org)
- Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. (elsevier.com)
- This length difference is uniquely due to smaller introns. (elsevier.com)
- 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)
- 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)
- Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. (biomedcentral.com)
- However, the relationship between intron length and GC content appears to be complicated. (biomedcentral.com)
- with and without quality information, splice site predictions, and intron length information. (biomedcentral.com)
- In contrast, the density of introns in a gene does not strongly depend on the level of gene expression. (nih.gov)
- As a result, the factors controlling gene expression and regulation impose a selective constraint on intron size [ 17 ]. (biomedcentral.com)
- The longer allele with 21 repeats showed an 80% reduction of gene expression compared with the shorter allele with 16 repeats. (aacrjournals.org)
- First, shorter introns tend to have higher recombination rates  . (plos.org)
- In silico analysis predicts the disappearance of the splicing donor site in intron 9, confirmed by patient peripheral leukocyte cP450arom and in vitro studies. (figshare.com)
- The gene structure consists of 60 exons/alternative exons and 40 distinct introns. (atlasgeneticsoncology.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)
- Molecular analysis of the STAT5b gene revealed a novel homozygous deletion of a G at the junction of exon 13-intron 13. (elsevier.com)
- 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)
- The GREB1 gene is located on the short arm of chromosome 2, at 2q25.1, between the genomic sites for E2F transcription factor 6 and neurotensin receptor 2 (Entrez gene 9687). (atlasgeneticsoncology.org)
- These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism. (fujita-hu.ac.jp)
- The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. (geoscience.net)
- SF3b (U2 snRNP component) is involved in splicing of these 3 ultra-short introns. (geoscience.net)
- Splicing of the 56-nt intron requires the U1, U2, and U4 snRNPs. (geoscience.net)
- Group III introns are proposed to be a fifth family, but little is known about the biochemical apparatus that mediates their splicing. (wikipedia.org)
- For example, it has been established that introns contain codes involved in the regulation of alternative splicing (e.g. (evolutionnews.org)
- Compared to the well characterized endonuclease-mediated intron homing, reverse splicing is less specific and represents a likely explanation for many intron transpositions into new genomic sites. (biomedsearch.com)
- The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. (ebi.ac.uk)
- 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)
- 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)
- After the introns are removed, the remaining exons are spliced together, not unlike splicing together pieces of film and leaving some on the cutting room floor. (mskcc.org)
- Alternative splicing can also change intron/exon size [ 16 ]. (biomedcentral.com)
- of Oregon), 'Genetic analysis of group II intron splicing in chloroplasts' MONDAY p.m. (bio.net)
- They appear to be related to group II introns, and possibly to spliceosomal introns. (wikipedia.org)
- The varieties of functional elements in introns are revealed to associate with the function of adjacent exons [ 11 ]. (biomedcentral.com)
- The genomic location of GREB1 on the short arm of chromosome 2. (atlasgeneticsoncology.org)
- In confirmation of prior studies, the shorter allele 16 was the most common allele in Caucasians (43%) and African-Americans (42%), but its frequency was significantly lower in Asians (average 17%, P = 10 −7 compared with Caucasians). (aacrjournals.org)
- Although functional, the extra gene lacks certain parts of the DNA code, called introns, found in normal genes. (genome.gov)
- After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. (biomedcentral.com)
- 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)
- The types of junk DNA include introns, pseudogenes, and mobile and repetitive DNAs. (creation.com)
- Sandwalk: Are introns mostly junk? (blogspot.com)
- Are introns mostly junk? (blogspot.com)
- There are many reasons for thinking that introns are mostly junk DNA. (blogspot.com)
- The authors are ignoring all the evidence suggesting that introns are mostly junk and concentrating on the relatively few examples where they have acquired a function. (blogspot.com)
- We know very little about how microRNAs located within introns are regulated and how they interact with their host genes," Eisfeld says. (eurekalert.org)