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.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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)
The relationships of groups of organisms as reflected by their genetic makeup.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Any method used for determining the location of and relative distances between genes on a chromosome.
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 complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Proteins, usually projecting from the cilia of olfactory receptor neurons, that specifically bind odorant molecules and trigger responses in the neurons. The large number of different odorant receptors appears to arise from several gene families or subfamilies rather than from DNA rearrangement.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
The genetic complement of a BACTERIA as represented in its DNA.
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The 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.
A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
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).
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.
Large regions of the GENOME that contain local similarities in BASE COMPOSITION.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
A type II keratin that is found associated with the KERATIN-10 in terminally differentiated epidermal cells such as those that form the stratum corneum. Mutations in the genes that encode keratin-1 have been associated with HYPERKERATOSIS, EPIDERMOLYTIC.
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.
The sequential location of genes on a chromosome.
Genus of BACTERIA in the family Frankiaceae. They are nitrogen-fixing root-nodule symbionts of many species of woody dicotyledonous plants.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Organizations representing specialized fields which are accepted as authoritative; may be non-governmental, university or an independent research organization, e.g., National Academy of Sciences, Brookings Institution, etc.
Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.
A superfamily of proteins containing the globin fold which is composed of 6-8 alpha helices arranged in a characterstic HEME enclosing structure.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.
Databases devoted to knowledge about specific genes and gene products.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
An unpleasant sensation induced by noxious stimuli which are detected by NERVE ENDINGS of NOCICEPTIVE NEURONS.
The TARSAL BONES; METATARSAL BONES; and PHALANGES OF TOES. The tarsal bones consists of seven bones: CALCANEUS; TALUS; cuboid; navicular; internal; middle; and external cuneiform bones. The five metatarsal bones are numbered one through five, running medial to lateral. There are 14 phalanges in each foot, the great toe has two while the other toes have three each.
A form of therapy that employs a coordinated and interdisciplinary approach for easing the suffering and improving the quality of life of those experiencing pain.
Scales, questionnaires, tests, and other methods used to assess pain severity and duration in patients or experimental animals to aid in diagnosis, therapy, and physiological studies.
Amount of stimulation required before the sensation of pain is experienced.
Stones in the KIDNEY, usually formed in the urine-collecting area of the kidney (KIDNEY PELVIS). Their sizes vary and most contains CALCIUM OXALATE.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.

Mouse trp2, the homologue of the human trpc2 pseudogene, encodes mTrp2, a store depletion-activated capacitative Ca2+ entry channel. (1/1104)

Capacitative Ca2+ entry (CCE) is Ca2+ entering after stimulation of inositol 1,4,5-trisphosphate (IP3) formation and initiation of Ca2+ store depletion. One hallmark of CCE is that it can also be triggered merely by store depletion, as occurs after inhibition of internal Ca2+ pumps with thapsigargin. Evidence has accumulated in support of a role of transient receptor potential (Trp) proteins as structural subunits of a class of Ca2+-permeable cation channels activated by agonists that stimulate IP3 formation-very likely through a direct interaction between the IP3 receptor and a Trp subunit of the Ca2+ entry channel. The role of Trp's in Ca2+ entry triggered by store depletion alone is less clear. Only a few of the cloned Trp's appear to enhance this type of Ca2+ entry, and when they do, the effect requires special conditions to be observed, which native CCE does not. Here we report the full-length cDNA of mouse trp2, the homologue of the human trp2 pseudogene. Mouse Trp2 is shown to be readily activated not only after stimulation with an agonist but also by store depletion in the absence of an agonist. In contrast to other Trp proteins, Trp2-mediated Ca2+ entry activated by store depletion is seen under the same conditions that reveal endogenous store depletion-activated Ca2+ entry, i.e., classical CCE. The findings support the general hypothesis that Trp proteins are subunits of store- and receptor-operated Ca2+ channels.  (+info)

Low-copy repeats mediate the common 3-Mb deletion in patients with velo-cardio-facial syndrome. (2/1104)

Velo-cardio-facial syndrome (VCFS) is the most common microdeletion syndrome in humans. It occurs with an estimated frequency of 1 in 4, 000 live births. Most cases occur sporadically, indicating that the deletion is recurrent in the population. More than 90% of patients with VCFS and a 22q11 deletion have a similar 3-Mb hemizygous deletion, suggesting that sequences at the breakpoints confer susceptibility to rearrangements. To define the region containing the chromosome breakpoints, we constructed an 8-kb-resolution physical map. We identified a low-copy repeat in the vicinity of both breakpoints. A set of genetic markers were integrated into the physical map to determine whether the deletions occur within the repeat. Haplotype analysis with genetic markers that flank the repeats showed that most patients with VCFS had deletion breakpoints in the repeat. Within the repeat is a 200-kb duplication of sequences, including a tandem repeat of genes/pseudogenes, surrounding the breakpoints. The genes in the repeat are GGT, BCRL, V7-rel, POM121-like, and GGT-rel. Physical mapping and genomic fingerprint analysis showed that the repeats are virtually identical in the 200-kb region, suggesting that the deletion is mediated by homologous recombination. Examination of two three-generation families showed that meiotic intrachromosomal recombination mediated the deletion.  (+info)

Comparisons of genomic structures and chromosomal locations of the mouse aldose reductase and aldose reductase-like genes. (3/1104)

Aldose reductase (AR), best known as the first enzyme in the polyol pathway of sugar metabolism, has been implicated in a wide variety of physiological functions and in the etiology of diabetic complications. We have determined the structures and chromosomal locations of the mouse AR gene (Aldor1) and of two genes highly homologous to Aldor1: the fibroblast growth factor regulated protein gene (Fgfrp) and the androgen regulated vas deferens protein gene (Avdp). The number of introns and their locations in the mouse Aldor1 gene are identical to those of rat and human AR genes and also to those of Fgfrp and Avdp. Mouse Aldor1 gene was found to be located near the Cald1 (Caldesmon) and Ptn (Pleiotropin) loci at the proximal end of chromosome 6. The closely related genes Fgfrp and Avdp were also mapped in this region of the chromosome, suggesting that these three genes may have arisen by a gene duplication event.  (+info)

Organization and alternate splice products of the gene encoding nuclear inhibitor of protein phosphatase-1 (NIPP-1). (4/1104)

Nuclear inhibitor of protein phosphatase-1 (NIPP-1) is one of two major regulatory subunits of protein phosphatase-1 in mammalian nuclei. We report here the cloning and structural characterization of the human NIPP-1 genes, designated PPP1R8P and PPP1R8 in human gene nomenclature. PPP1R8P (1.2 kb) is a processed pseudogene and was localized by in situ hybridization to chromosome 1p33-32. PPP1R8 is an authentic NIPP-1 gene and was localized to chromosome 1p35. PPP1R8 (25.2 kb) is composed of seven exons and encodes four different transcripts, as determined from cDNA library screening, reverse transcriptase-PCR (RT-PCR) and/or EST (expressed sequence tag) database search analysis. NIPP-1alpha mRNA represents the major transcript in human tissues and various cell lines, and encodes a polypeptide of 351 residues that only differs from the previously cloned calf thymus NIPP-1 by a single residue. The other transcripts, termed NIPP-1beta, gamma and delta, are generated by alternative 5'-splice site usage, by exon skipping and/or by alternative polyadenylation. The NIPP-1beta/delta and NIPP-1gamma mRNAs are expected to encode fragments of NIPP-1alpha that differ from the latter by the absence of the first 142 and 224 residues, respectively. NIPP-1gamma corresponds to 'activator of RNA decay-1' (Ard-1) which, unlike NIPP-1alpha, displays in vitro and endoribonuclease activity and lacks an RVXF consensus motif for interaction with protein phosphatase-1. While the NIPP-1alpha/beta/delta-transcripts were found to be present in various human tissues, the NIPP-1gamma transcript could only be detected in human transformed B-lymphocytes.  (+info)

The mouse p97 (CDC48) gene. Genomic structure, definition of transcriptional regulatory sequences, gene expression, and characterization of a pseudogene. (5/1104)

Here we present the first description of the genomic organization, transcriptional regulatory sequences, and adult and embryonic gene expression for the mouse p97(CDC48) AAA ATPase. Clones representing two distinct p97 genes were isolated in a genomic library screen, one of them likely representing a non-functional processed pseudogene. The coding region of the gene encoding the functional mRNA is interrupted by 16 introns and encompasses 20.4 kilobase pairs. Definition of the transcriptional initiation site and sequence analysis showed that the gene contains a TATA-less, GC-rich promoter region with an initiator element spanning the transcription start site. Cis-acting elements necessary for basal transcription activity reside within 410 base pairs of the flanking region as determined by transient transfection assays. In immunohistological analyses, p97 was widely expressed in embryos and adults, but protein levels were tightly controlled in a cell type- and cell differentiation-dependent manner. A remarkable heterogeneity in p97 immunostaining was found on a cellular level within a given tissue, and protein amounts in the cytoplasm and nucleus varied widely, suggesting a highly regulated and intermittent function for p97. This study provides the basis for a detailed analysis of the complex regulation of p97 and the reagents required for assessing its functional significance using targeted gene manipulation in the mouse.  (+info)

Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN. (6/1104)

PTEN/MMAC1 is a recently characterized tumor suppressor. A pseudogene derived from the human PTEN/MMAC1 phosphatase, psiPTEN, has been reported. Recent analysis of the pseudogene revealed conflicting results about the expression of psiPTEN. In this study, we show that the PTEN/MMAC1 pseudogene is actively transcribed in all cells and tissues examined. In some cases, pseudogene transcripts were found to represent as much as 70% of the total PTEN/MMAC1 RNA. As psiPTEN is transcribed, there is a potential for misinterpretation of PTEN/MMAC1 mutations when RT-PCR techniques are used, as well as potential for a psiPTEN-encoded translation product. Although we were unable to detect a pseudogene protein product in the cell lines examined, a baculovirus produced GST pseudogene fusion protein exhibited phosphatase activity comparable to wild type. The results of this study, taken together, indicate the potential complication of PTEN/MMAC1 molecular analysis caused by the expression of psiPTEN.  (+info)

Cloning of mouse sepiapterin reductase gene and characterization of its promoter region. (7/1104)

We have isolated and characterized approximately 5 kb mouse sepiapterin reductase gene (Spr) and a highly homologous pseudogene (Sprp). The authentic Spr gene is present as a single copy in the mouse genome and is composed of three exons containing the entire coding region. The primer extension experiment located the transcription initiation site in a putative pyrimidine-rich Inr element. The promoter region of the Spr gene is embedded within a CpG island. It was shown that the promoter region is devoid of distinctive TATA and CAAT boxes. Transient transfection of a series of 5' deletion derivatives of the Spr promoter showed the sequence between -83 and -51 to be essential for promoter activity. The pseudogene Sprp lacks promoter region and exon 3.  (+info)

The fhu genes of Rhizobium leguminosarum, specifying siderophore uptake proteins: fhuDCB are adjacent to a pseudogene version of fhuA. (8/1104)

A mutant of Rhizobium leguminosarum was isolated which fails to take up the siderophore vicibactin. The mutation is in a homologue of fhuB, which in Escherichia coli specifies an inner-membrane protein of the ferric hydroxamate uptake system. In Rhizobium, fhuB is in an operon fhuDCB, which specifies the cytoplasmic membrane and periplasmic proteins involved in siderophore uptake. fhuDCB mutants make vicibactin when grown in Fe concentrations that inhibit its production in the wild-type. Nodules on peas induced by fhuDCB mutants were apparently normal in N2 fixation. Transcription of an fhuDCB-lacZ fusion was Fe-regulated, being approximately 10-fold higher in Fe-depleted cells. Downstream of fhuB, in the opposite orientation, is a version of fhuA whose homologues in other bacteria specify hydroxamate outer-membrane receptors. This fhuA gene appears to be a pseudogene with stop codons and undetectable expression.  (+info)

According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological
Over time, some gene copies mutate to lose their function entirely. Such so-called pseudogenes may arise through accumulation of mutations that A gene family is descended from a common ancestral gene. prevent translation of the gene, such as an insertion or deletion that stops translation at the beginning of the gene sequence. Pseudogenes also arise from mutation in a genes promoter region. The promoter is the site at the beginning of the gene that attracts the enzyme called RNA polymerase. Without a functional promoter, the gene cannot be transcribed effectively, and so cannot lead to protein production.. Retroposition is a very common source of pseudogenes. Pseudogenes have been discovered because their sequences are similar to functional genes. In humans, pseudogenes are known to exist for topoisomerase (a gene that cuts DNA to prevent twisting), ferritin (an iron storage protein), two different forms of actin, and many other genes.. ...
Functional and pseudogenes are similarly organized and may equally contribute to the extensive antibody diversity of the IgVHII family.: Eleven germ-line immuno
The MHC contains many HLA class 1 and class 1 like DNA sequences. These include the classical class 1 genes (HLA-A, -B and -C), the nonclassical class 1 genes (HLA-E, -F and -G) and the so-called Class 1 non-expressed or pseudogenes (HLA-H, -K, -J, -L and many others). Relative to the other Class 1 genes, the pseudogenes have been understudied, largely, (and as their name suggests) as a result of the assumption that these genes have no function. However, a recent study (Paganini et al, 2019) has identified that some HLA-H alleles have all the elements expected of a functional HLA class 1 gene. This begs the questions. Is HLA-H functional? What is its function? Could other pseudogenes (HLA Class 1, HLA Class 2, MIC and others) be functional on some haplotypes? Could these pseudogenes be mismatched in transplantation? If so - what is the impact ...
TY - JOUR. T1 - Transcribed processed pseudogenes in the human genome. T2 - An intermediate form of expressed retrosequence lacking protein-coding ability. AU - Harrison, Paul M.. AU - Zheng, Deyou. AU - Zhang, Zhaolei. AU - Carriero, Nicholas. AU - Gerstein, Mark. PY - 2005/11/3. Y1 - 2005/11/3. N2 - Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete protein-coding sequences. Processed pseudogenes (TPψgs) are made through mRNA retrotransposition. There is overwhelming genomic evidence for thousands of human Pψgs and also dozens of human processed genes that comprise complete retrotransposed copies of other genes. Here, we survey for an intermediate entity, the transcribed processed pseudogene (TPψg), which is disabled but nonetheless transcribed. TPψgs may affect expression of paralogous genes, as observed in the case of the mouse makorin1-p1 ...
Pseudogenes are DNA sequences that resemble functional genes but seem to have no purpose. The presence of similar eta globin pseudogenes in humans and chimps has been used as an argument for common ancestry of the two species.
Our understanding of cancer pathways has been changed by the determination of noncoding transcripts in the human genome in recent years. miRNAs and pseudogenes are key players of the noncoding transcripts from the genome, and alteration of their expression levels provides clues for significant biomarkers in pathogenesis of diseases. Especially, miRNAs and pseudogenes have both oncogenic and tumor-suppressive roles in each step of cancer tumorigenesis. In this current study, association between oncogenes and miRNAs-pseudogenes was reviewed and determined in human cancer by the CellMiner web-tool. © 2018, Springer Science+Business Media LLC ...
Full Text - Background: Growing studies have reported that pseudogenes play key roles in multiple human cancers. However, expression and roles of pseudogenes in renal cell carcinoma remains absent.Results: 31 upregulated and 16 downregulated pseudogenes were screened. Higher expression of DUXAP8 and DUXAP9 indicated poorer prognosis of kidney cancer. 33 and 5 miRNAs were predicted to potentially binding to DUXAP8 and DUXAP9, respectively. miR-29c-3p was identified as the most potential binding miRNAs of DUXAP8 and DUXAP9 based on expression, survival and correlation analyses. 254 target genes of miR-29c-3p were forecast. 47 hub genes with node degree >= 10 were identified. Subsequent analysis for the top 10 hub genes demonstrated that COL1A1 and COL1A2 may be two functional targets of DUXAP8 and DUXAP9. Expression of DUXAP8, DUXAP9, COL1A1 and COL1A2 were significantly increased in cancer samples compared to normal controls while miR-29c-3p expression was decreased. Luciferase reporter assay revealed
Background: Growing studies have reported that pseudogenes play key roles in multiple human cancers. However, expression and roles of pseudogenes in renal cell carcinoma remains absent.Results: 31 upregulated and 16 downregulated pseudogenes were screened. Higher expression of DUXAP8 and DUXAP9 indicated poorer prognosis of kidney cancer. 33 and 5 miRNAs were predicted to potentially binding to DUXAP8 and DUXAP9, respectively. miR-29c-3p was identified as the most potential binding miRNAs of DUXAP8 and DUXAP9 based on expression, survival and correlation analyses. 254 target genes of miR-29c-3p were forecast. 47 hub genes with node degree >= 10 were identified. Subsequent analysis for the top 10 hub genes demonstrated that COL1A1 and COL1A2 may be two functional targets of DUXAP8 and DUXAP9. Expression of DUXAP8, DUXAP9, COL1A1 and COL1A2 were significantly increased in cancer samples compared to normal controls while miR-29c-3p expression was decreased. Luciferase reporter assay revealed that miR
Within a population, the pseudogenization of a gene does not happen instantaneously. Rather, after a disruptive mutation occurs, the alleles at the locus undergo a fixation process. Depending on the outcome, such a mutation is either fixed or lost. Thus, every gene loss goes through two stages: a polymorphic stage in the contemporary population subject to evolutionary forces; and a fixed stage freed from selective pressure. The fixed mutation becomes the base substitution in the species under study relative to the other and is identified through comparison of the genomes of two species. By comparing the human and the mouse genomes, we identify 76 fixed unitary pseudogenes. In addition, we identify 11 human genes with pseudogenic alleles, whose disruptive mutations include nonsense mutations and frameshifts. Our identification of polymorphic pseudogenes is by no means comprehensive as we search in the reference genome sequence for only the loci that are associated with both CDS disruptions and ...
Complete information for RNU6V gene (Pseudogene), RNA, U6 Small Nuclear Variant Sequence With SNRPE Pseudogene Sequence, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Number of pseudogenes per paralogous family. Pseudogenes were associated with paralogous families, based on their parents. Families discussed in the text are la
Pseudofam is a database of pseudogenes assigned to different protein families which currently represents a compilation of pseudogenes, as well as their families, identified from 10 eukaryotic genomes. More... ...
Transcription factor pseudogenes have not been systematically studied before. Nuclear receptors (NRs) constitute one of the largest groups of transcription factors in animals (e.g., 48 NRs in human). The availability of whole-genome sequences enables a global inventory of the NR pseudogenes in a num …
Metabolic rates of cancer cells are faster compared to normal cells. This faster rate yields aberrant protein folding and causes loss of protein function. Therefore, cancer cells need more Heat Shock Proteins (HSPs) for proper substrate- protein folding on oncogenic pathways. Pseudogenes regulate tumor suppressors and oncogenes, and pseudogenes are deregulated in cancer progression. Further, alterations in miRNA expression have been identified in different cancer types. MiRNAs also have both oncogenic and tumour-suppressive roles in breast cancer post-transcriptional gene regulation. Breast cancer is a genetic disease and we performed miRNA analysis in human breast cancer cell lines to identify miRNAs in association with HSPs and pseudogenes by employing CellMiner; a web-based suite. CellMiner integrates several databases and help analysing microarray metadata. The experimental data provide a platform for researchers to compare macromolecules relationships in NCI-60 cell lines. Breast cancer ...
Current screening practices have been able to identify PMS2 mutations in 78 % of cases of colorectal cancer from the Colorectal Cancer Family Registry (Colon CFR) which showed solitary loss of the PMS2 protein. However the detection of large-scale deletions in the 3′ end of the PMS2 gene has not been possible due to technical difficulties associated with pseudogene sequences. Here, we utilised a recently described MLPA/long-range PCR-based approach to screen the remaining 22 % (n = 16) of CRC-affected probands for mutations in the 3′ end of the PMS2 gene. No deletions encompassing any or all of exons 12 through 15 were identified; therefore, our results suggest that 3′ deletions in PMS2 are not a frequent occurrence in such families ...
A large number of pseudogenes have been found to be transcribed in human cancers. However, only a few pseudogenes are functionally characterized. Here, we identified a transcribed pseudogene of vascular endothelial growth factor receptor-1 (VEGFR1), or fmsrelated tyrosine kinase 1 (FLT1), in human colorectal cancer (CRC) cells. Interestingly, this pseudogene (designated as FLT1P1) was found to be transcribed bidirectionally and functionally modulated cognate VEGFR1 protein expression in the cells. Mechanistically, expression of FLT1P1 antisense transcript not only inhibited the VEGFR1 expression, but also inhibited non-cognate VEGF-A expression through interaction with miR-520a. Perturbation of FLT1P1 expression by RNA interference (RNAi) markedly inhibited tumor cell proliferation and xenograft tumor growth. This study identifies FLT1P1 antisense as a critical regulator of VEGFR1 and VEGF-A expression in CRC cells, and highlights its role in regulation of the pathogenesis of CRC. Implications: ...
4. students should know that the pictures were faked: This goes without saying. Since biologists have known since the 1980s that peppered moths do not normally rest on tree trunks, not to tell students that the pictures were staged (in many cases by gluing or pinning dead moths to desired backgrounds) constitutes as clear a case of scientific fraud as any on record. Yet Im aware of no sincere efforts by Darwinists to inform students of this -- despite their pious declarations of good intentions. Almost all recent (1998-2000) biology textbooks use such photos without any indication that they were staged. As a scientist, I find this absolutely inexcusable. If dogmatic Darwinists were as smart as they pretend to be, they would be actively campaigning -- for their own good! -- to rid textbooks of this fraud. Acquiescence in scientific misconduct will not look good on their resumes ...
A pseudogene is a gene copy that does not produce a functional, full-length protein. The human genome is estimated to contain up to 20,000 pseudogenes. Although much effort has been devoted to understanding the function of pseudogenes, their biological roles remain largely unknown. Here we report the role of an expressed pseudogene regulation of messenger-RNA stability in a transgene-insertion mouse mutant exhibiting polycystic kidneys and bone deformity. The transgene was integrated into the vicinity of the expressing pseudogene of Makorin1, called Makorin1-p1. This insertion reduced transcription of Makorin1-p1, resulting in destabilization of Makorin1 mRNA in trans by way of a cis-acting RNA decay element within the 5 region of Makorin1 that is homologous between Makorin1 and Makorin1-p1. Either Makorin1 or Makorin1-p1 transgenes could rescue these phenotypes. Our findings demonstrate a specific regulatory role of an expressed pseudogene, and point to the functional significance of ...
The accuracy of the DNA sequence is critical to scientists who study diseases linked to chromosome 22, such as the DiGeorge syndrome. Infants born with this rare condition are missing a large portion of chromosome 22. As a result, they develop recurrent infections and heart problems. When youre working on a chromosomal region where a gene for a disease has been mapped, its important to know exactly which genes are in that region, says Dunham, who also worked on the original sequence. The new analysis, he believes, makes it fairly certain that scientists now know all of the genes on chromosome 22 that code for proteins. The findings appear in Genome Research. When the new analysis of chromosome 22 was completed, the total number of known genes increased only by one, to 546. But the number of pseudogenes more than doubled (to 234). Pseudogenes are gene-like stretches of DNA that apparently are not real genes; it is not clear what these pseudogenes do or why they are there.. The researchers ...
Hi all, I used spades for assembly of bacteria-Illumina reads, and galaxy-Prokka for annotation Visualization of the annotation results showed me:. Summary of the active entries: contigs: 65. bases: 5736331. CDS: 5102. gene: 5279. misc_RNA: 52. rRNA: 9. tRNA: 115. tmRNA: 1. 1- how can I confirm that annotation results are correct? 2- I am confused, why there are no pseudogenes in my report!! Thanks for your time ...
Pseudogenes page of Was Darwin right? A site devoted to scientific arguments to support intelligent design or Creation, rather than evolution
MGI protein superfamily detail pages represent the protein classification set for a homeomorphic superfamily from the Protein Information Resource SuperFamily (PIRSF) site.. Mouse superfamily members are shown with links to their corresponding HomoloGene Classes. Note that pseudogenes are included in PIRSF families but not in orthology sets used here. You can select a given mouse superfamily member and download (or forward to NCBI BLAST) FASTA formatted protein sequences of that mouse gene and its mouse, human and rat homologs, as defined in the corresponding HomoloGene Class. The numbers of mouse, human and rat genes in the HomoloGene Class are shown. You can also Select all mouse superfamily members to obtain their protein sequences and the protein sequences for all mouse, human and rat homologs of the mouse superfamily members.. The number of protein sequences returned does not always match the numbers of homologs shown, because the same protein sequence can be associated with multiple ...
MGI protein superfamily detail pages represent the protein classification set for a homeomorphic superfamily from the Protein Information Resource SuperFamily (PIRSF) site.. Mouse superfamily members are shown with links to their corresponding HomoloGene Classes. Note that pseudogenes are included in PIRSF families but not in orthology sets used here. You can select a given mouse superfamily member and download (or forward to NCBI BLAST) FASTA formatted protein sequences of that mouse gene and its mouse, human and rat homologs, as defined in the corresponding HomoloGene Class. The numbers of mouse, human and rat genes in the HomoloGene Class are shown. You can also Select all mouse superfamily members to obtain their protein sequences and the protein sequences for all mouse, human and rat homologs of the mouse superfamily members.. The number of protein sequences returned does not always match the numbers of homologs shown, because the same protein sequence can be associated with multiple ...
This gene encodes a multifunctional protein that is involved in various cellular processes, including gene expression, cell signaling, and RNA processing and transport. The protein includes an N-terminal transcriptional activation domain and a C-terminal RNA-binding domain. Chromosomal translocations between this gene and various genes encoding transcription factors result in the production of chimeric proteins that are involved in tumorigenesis. These chimeric proteins usually consist of the N-terminal transcriptional activation domain of this protein fused to the C-terminal DNA-binding domain of the transcription factor protein. Mutations in this gene, specifically a t(11;22)(q24;q12) translocation, are known to cause Ewing sarcoma as well as neuroectodermal and various other tumors. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 1 and 14. [provided by RefSeq, Jul 2009 ...
Pseudogenes have a reputation of being evolutionary relics or junk DNA. While they are well characterized in mammals, studies in more complex plant genomes were so far hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole genome assessment of pseudogenes on the barley genome. We identified, characterized, and classified 89,440 gene fragments and pseudogenes, scattered along the chromosomes with occasional hotspots and higher densities at the chromosome ends ...
I think that what we have here is the fact that the same object can be classified in different ways. In regards to structural yet not functional similarity to a functional gene, we classify something as a pseudogene. This seems to be a instance of a genome feature that has a function in a different way that that associated with its homolog. So in one classification/definition it is a gene [functional genome feature]. In another, its a pseudogene [see definition below]. I would think perhaps that when a feature classified as a pseudogene is determined to have a function, it would be reclassified...... Judy val at sanger.ac.uk wrote: ,But there is alway one.... , ,PMID: 12721631 , ,Nature. 2003 May 1;423(6935):91-6. , ,An expressed pseudogene regulates the messenger-RNA stability of its homologous ,coding gene. ,Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, ,Wynshaw-Boris A, Yoshiki A , , , , , ,Quoting chris mungall ,cjm at fruitfly.org,: , , , ,,Yes, I agree. ...
Hi I have a question along the lines of Vals comment. I was wondering what the scientific community would expect to see with respect to how a pseudogene that expresses a transcript would be annotated in SO. Suzi has said that if a pseudogene is discovered to express a transcript, than the pseudogene annotation should be removed and replaced with something else, i.e. ncRNA. However, is that consistent with what the people studying these do, i.e. if they discover that a pseudogene is expressed, do they stop calling it a pseudogene? Im not sure that they do. In the exposure to this issue that Ive had, it seems that people DO continue to call it a pseudogene, but add the adjective expressed so that they now refer to it as an expressed pseudogene. If this is common practice, to refer to pseudogenes, i.e. genes that dont express the product they might have been expected to based on sequence similarity to a functional gene, that actually do express a product, often an ncRNA, as ...
This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. The encoded protein also functions in mitochondrial DNA replication and repair. Sequence polymorphisms in this gene are associated with Alzheimers and Parkinsons diseases. There are pseudogenes for this gene on chromosomes 6, 7, and 11. Alternative splicing results in multiple transcript variants ...
This gene encodes a subunit of the condensin complex, which is responsible for the condensation and stabilization of chromosomes during mitosis and meiosis. Phosphorylation of the encoded protein activates the condensin complex. There are pseudogenes for this gene on chromosomes 8 and 15. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012] ...
This gene encodes a member of a family of adenosine triphosphate(ATP)-metabolizing molecular chaperones with roles in stabilizing and folding other proteins. The encoded protein is localized to melanosomes and the endoplasmic reticulum. Expression of this protein is associated with a variety of pathogenic states, including tumor formation. There is a microRNA gene located within the 5 exon of this gene. There are pseudogenes for this gene on chromosomes 1 and 15. [provided by RefSeq, Aug 2012 ...
TY - JOUR. T1 - Whole-genome tiling array analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions. AU - Akama, Takeshi. AU - Suzuki, Koichi. AU - Tanigawa, Kazunari. AU - Kawashima, Akira. AU - Wu, Huhehasi. AU - Nakata, Noboru. AU - Osana, Yasunori. AU - Sakakibara, Yasubumi. AU - Ishii, Norihisa. PY - 2009/5/1. Y1 - 2009/5/1. N2 - Whole-genome sequence analysis of Mycobacterium leprae has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some M. leprae pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the M. leprae genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with M. leprae RNA from the SHR/NCrj-rnu nude rat, and the results were compared to results from an open reading ...
Molecular properties of odorant compounds essential for activation of the human olfactory receptor hOR17-40 were investigated using a collection of 23 variants of its cognate ligand helional. Coupling receptor activation to an optically detectable intracellular Ca(2+) ion flux allowed dose-dependent …
The neutrophil cytosolic factor 1 (NCF1) gene encodes the 47 kDa cytosolic subunit of neutrophil NADPH oxidase, which produces superoxide anion. The NCF1 gene is located in close proximity to two highly similar, multi-exon pseudogenes at chromosome 7q11.23, corresponding to this gene record and GeneID:654816. The two pseudogenes contain a dinucleotide deletion (delta-GT) in exon 2 that results in a frameshift and truncation of the open reading frame, and neither pseudogene is likely to express a protein. Recombination events between the pseudogenes and the functional NCF1 gene can inactivate the NCF1 gene and result in chronic granulomatous disease. [provided by RefSeq, Nov 2009]
The ant Atta sexdens is widely spread in the Americas and is a pest of several crops like citrus and cane sugar. Due to the divergent aspects of the last morphological revisions, there are still doubts whether Atta sexdens is a single species or a group of cryptic species. Studies based on molecular characters are more accurate for assessing the phylogeny of populations or lineages even close. However, these studies are often hampered in their course by co-amplification of numts, which are nuclear pseudogenes of mitochondrial origin and that can lead to misinterpretation of phylogenetic relationships were analyzed together with its counterpart in mitochondria. Therefore, in this paper, we present two chapters, where we looked first at 100 nests of A. sexdens collected throughout the American continent in order to verify the existence of cryptic species, together with the time of divergence between them, assessing the utility of nuclear and mitochondrial markers in studies of this nature, and in ...
Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system - Volume 98 Issue 3 - G. Dunshea, N.B. Barros, R.S. Wells, N.J. Gales, M.A. Hindell, S.N. Jarman
Retrogenes inserted into the genome since the mouse/human divergence show a break in the human genome syntenic net alignments to the mouse genome. A break in orthology score is calculated and weighted before contributing to the final retrogene score. The break in orthology score ranges from 0-130 and it represents the portion of the genome that is missing in each species relative to the reference genome (human hg38) at the retrogene locus as defined by syntenic alignment nets. If the score is 0, there is orthologous DNA and no break in ortholog with the other species; this could be an ancient retrogene; duplicated pseudogenes may also score low because they are often generated via large segmental duplication events so the size of the pseudogene is small relative to the size of the inserted duplicated sequence. Scores greater than 100 represent cases where the retrogene alignment has no flanking alignment resulting from an ancient insertion or other complex rearrangement. Breaks in orthology with ...
RefSeq Summary (NM_001675): This gene encodes a transcription factor that was originally identified as a widely expressed mammalian DNA binding protein that could bind a tax-responsive enhancer element in the LTR of HTLV-1. The encoded protein was also isolated and characterized as the cAMP-response element binding protein 2 (CREB-2). The protein encoded by this gene belongs to a family of DNA-binding proteins that includes the AP-1 family of transcription factors, cAMP-response element binding proteins (CREBs) and CREB-like proteins. These transcription factors share a leucine zipper region that is involved in protein-protein interactions, located C-terminal to a stretch of basic amino acids that functions as a DNA binding domain. Two alternative transcripts encoding the same protein have been described. Two pseudogenes are located on the X chromosome at q28 in a region containing a large inverted duplication. [provided by RefSeq, Sep 2011 ...
The protein encoded by this gene, Aldolase A (fructose-bisphosphate aldolase), is a glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Three aldolase isozymes (A, B, and C), encoded by three different genes, are differentially expressed during development. Aldolase A is found in the developing embryo and is produced in even greater amounts in adult muscle. Aldolase A expression is repressed in adult liver, kidney and intestine and similar to aldolase C levels in brain and other nervous tissue. Aldolase A deficiency has been associated with myopathy and hemolytic anemia. Alternative splicing and alternative promoter usage results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 3 and 10 ...
This gene encodes a member of the FXYD family of transmembrane proteins. This particular protein encodes phosphohippolin, which likely affects the activity of Na,K-ATPase. Multiple alternatively spliced transcript variants encoding the same protein have been described. Related pseudogenes have been identified on chromosomes 10 and X. Read-through transcripts have been observed between this locus and the downstream sodium/potassium-transporting ATPase subunit gamma (FXYD2, GeneID 486) locus.[provided by RefSeq, Feb 2011 ...
The human genome contains vast numbers of sequences that have copied themselves to new genomic locations by retrotransposition. Long Interspersed Nuclear Element-1 (LINE-1 or L1) is the only sequence in the human genome still capable of autonomous retrotransposition. L1 elements have contributed to the evolution of the human genome via insertional mutagenesis, pseudogene formation, sequence transduction, and recombination events (producing insertions, deletions and inversions). Currently general and L1- specific sequence databases do not reflect the true level of Full Length Human Specific L1 (FL-L1HS) variation, due to the polymorphic nature of these elements and the way the databases were compiled. Methods to identify FL-L1HS were applied to three sequence assemblies (Reference, Celera and HuRef) and the nucleotide accession database from NCBI. A non-redundant set of 533 FL-L1HS was discovered in these four sources, of which 164 resided in genes. The trace archives from Ensembl were also ...
There are 9 Pax genes in the human or mouse genomes, defined by presence of a 128 amino acid Paired domain, and of these 7 are members of the PRD homeobox class by virtue of possessing a homeobox: complete homeobox for PAX3, 4, 6 and 7; partial homeobox for PAX2, 5 and 8 (the two human Pax genes lacking a homeobox entirely are PAX1 and PAX9; these are not included in this database). In addition to these 7 homeobox-containing Pax genes, there are a further 43 PRD class genes in the human genome. These 50 genes can be divided into 31 gene families. There are also 24 human pseudogenes generated from these genes, plus an unknown number of DUX repetitive sequences (Holland et al. 2007 ...
There are 9 Pax genes in the human or mouse genomes, defined by presence of a 128 amino acid Paired domain, and of these 7 are members of the PRD homeobox class by virtue of possessing a homeobox: complete homeobox for PAX3, 4, 6 and 7; partial homeobox for PAX2, 5 and 8 (the two human Pax genes lacking a homeobox entirely are PAX1 and PAX9; these are not included in this database). In addition to these 7 homeobox-containing Pax genes, there are a further 43 PRD class genes in the human genome. These 50 genes can be divided into 31 gene families. There are also 24 human pseudogenes generated from these genes, plus an unknown number of DUX repetitive sequences (Holland et al. 2007 ...
This gene encodes a member of a small family of transcription factors that function through binding of DP interaction partner proteins. The encoded protein recognizes a specific sequence motif in DNA and interacts directly with the retinoblastoma protein (pRB) to regulate the expression of genes involved in the cell cycle. Altered copy number and activity of this gene have been observed in a number of human cancers. There are pseudogenes for this gene on chromosomes 2 and 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013 ...
Lipid antigens are presented to T cells by the CD1 family of proteins. In this study, we characterize the complete dog (Canis familiaris) CD1 locus, which is located on chromosome 38. The canine locus contains eight CD1A genes (canCD1A), of which five are pseudogenes, one canCD1B, one canCD1C, one canCD1D, and one canCD1E gene. In vivo expression of canine CD1 proteins was shown for canCD1a6, canCD1a8, and canCD1b, using a panel of anti-CD1 monoclonal antibodies (mAbs). CanCD1a6 and canCD1a8 are recognized by two distinct mAbs. Furthermore, we show differential transcription of the three canCD1A genes in canine tissues. In canine skin, the transcription level of canCD1A8 was higher than that of canCD1A6, and no transcription of canCD1A2 was detected. Based on protein modeling and protein sequence alignment, we predict that both canine CD1a proteins can bind different glycolipids in their groove. Besides differences in ectodomain structure, we observed the unique presence of three types of ...
This assay is not designed to detect deep intronic variants, balanced translocations, large inversions, mosaicism or complex genomic rearrangements. Homopolymer regions and rare polymorphisms under primer sites can affect the performance of the assay. The presence of pseudogenes can interfere with the ability to detect variants in certain genes. This assay is not intended for use in patients who have received allogeneic bone marrow transplants, as it may not reflect the germline genetic status of these patients.. This test was developed, and its performance characteristics determined, by LabCorp. It has not been cleared or approved by the US Food and Drug Administration (FDA). ...
The team identified 154 pseudogenes in the zebrafish genome, a fraction of the 13,000 or so pseudogenes found in the human genome. In fact, 70% of human genes are found in zebrafish . Practically speaking they offer many advantages as research models: The understanding of several human diseases has already grown leaps and bounds because of zebrafish studies. Disruption of enhancer function has been shown to lead to abnormal gene expression and thus to disease (2-4). The genetic underpinnings of heart development in zebrafish are highly similar to that in humans, while zebrafish presents many advantages that allow for rapid screening of … This paper focuses on … Hopkins and her colleagues found that a gene called met, which is known to cause cancer, sits on a chromosome found in excess in zebrafish tumors.,Other researchers had previously observed met on a chromosome found in extra numbers in human cancer. This high degree of similarity has led to the broad use of zebrafish to study the ...
Upon further investigation, however, Ive discovered that the Ensembl database appears to be inaccurate on that point, and its not confirmed that the GULO pseudogene produces a transcript (indeed, clicking on Supporting evidence, one finds that there is No Transcript supporting evidence for this transcript). Part of the reason for this is that the GULO pseudogene lacks a canonical promoter. However, that doesnt necessarily mean this pseudogene produces no RNA transcript. Many metazoan loci possess non-canonical promoters that, moreover, can be millions of base pairs upstream of annotated exons (e.g., see Manak et al., 2006). A further complication with the proposed hypothesis is that some exons are absent from the GULO pseudogene, and its not entirely clear to me how they could be created by RNA editing. While my original hypothesis is probably incorrect with respect to this particular pseudogene, it remains possible that the human GULO pseudogene yields RNAs that perform some other ...
Complete information for MRPS21P1 gene (Pseudogene), Mitochondrial Ribosomal Protein S21 Pseudogene 1, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
An example of the difficulty and complexity associated with pseudogene designation is observed when viewing the CDSs Cj0522, Cj0523 and Cj0524 within C. jejuni NCTC11168. These three CDSs are represented as one whole CDS on a single frame within C. jejuni RM1221 (Cje0628). The three CDSs are large enough to be represented as individual CDSs and in C. jejuni NCTC11168 have been represented on more than one frame. The question can be asked as to whether these CDSs (which are intact in C. jejuni RM1221), represent a pseudogene in C. jejuni NCTC11168. Given the fact that in C. jejuni RM1221 these three CDSs do actually code for a product (Na/Pi-cotransporter, putative), it is more likely that they represent a pseudogene in C. jejuni NCTC11168. In this re-annotation, our intention was to carry out a full mark up of existing pseudogenes, however, the potential for a pseudogene has been noted.. The frequency and importance of pseudogene formation in microorganisms has attained added significance in ...
The entire functional NANOG gene (according to our sequencing data) and NANOGP1 are present in both the human and chimpanzee genome assemblies at orthologous chromosomal positions. In the 3 UTR of the NANOG gene, there is an Alu element, which is missing from NANOGP1 in both genomes. Therefore, the NANOGP1 unprocessed pseudogene arose through duplication of the chromosomal region containing NANOG before the human-chimpanzee (H/C) divergence and before insertion of the Alu element into the NANOG gene. Because the same Alu element is present in both the human and chimpanzee NANOG genes, its insertion must also have preceded the H/C divergence. The processed pseudogenes NANOGP2, NANOGP3, NANOGP4, NANOGP5, NANOGP6, NANOGP7, NANOGP9, and NANOGP10 lack this Alu element. They thus likely arose before its insertion and, therefore, also predate the H/C divergence. The presence of the NANOGP11 pseudogene fragment in both the human and chimpanzee genomes likewise shows that its origin preceded H/C ...
Aldolase A (ALDOA, or ALDA), also known as fructose-bisphosphate aldolase, is an enzyme that in humans is encoded by the ALDOA gene on chromosome 16. The protein encoded by this gene is a glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Three aldolase isozymes (A, B, and C), encoded by three different genes, are differentially expressed during development. Aldolase A is found in the developing embryo and is produced in even greater amounts in adult muscle. Aldolase A expression is repressed in adult liver, kidney and intestine and similar to aldolase C levels in brain and other nervous tissue. Aldolase A deficiency has been associated with myopathy and hemolytic anemia. Alternative splicing and alternative promoter usage results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 3 and 10. [provided by RefSeq, Aug 2011] ALDOA is a homotetramer and one of the ...
BACKGROUND: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. RESULTS: The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has ...
2016 CONFERENCE AWARDS. AGTA is pleased to announce the recipients of the 2016 Conference Awards. Congratulations!. Early Career Researcher Prizes. Best Oral Presentation ($1,000) - Sam Buckberry, University of Western Australia, W.A. Characterising epigenome dynamics during the reprogramming of somatic cells to IPS Cells. Best Poster ($500) - Daniel Thomson, Garvan Institute of Medical Research. The Recycled Genome - RNA Captureseq reveals widespread expression of Human pseudogenes as chimeric gene isoforms. Student Prizes. Best Oral Presentation ($1,000) - Beth Signal, Garvan Institute of Medical Research, N.S.W ...
1) Because the use of a structure has not yet been discovered, it does not follow that none exists. Millers appeal is to a naturalistic explanation that assumes what it should be trying to prove - a kind of a naturalism of the gaps.. 2) Even if the pseudogenes have no function, that fact provides no explanation for how they arose in the first place. The simple reproduction of a pseudogene requires more than a dozen sophisticated proteins to separate, align, copy, reconfigure and reinsert nucleotides back into the DNA. Evolution provides no explanation for how such a process could have come to be.. 3) Implicitly required in Millers claim is an assumption that Intelligent Design proposes that these pseudogenes arose in the recent past. But Intelligent Design makes no such claim. The fact that a complex system shows evidence of being designed is completely devoid of any claim about when this might have taken place. ...
Amakawa R., Jing W., Ozawa K., Matsunami N., Hamaguchi Y., Matsuda F., Kawaichi M., Honjo T.. The mouse Igkjrb protein specifically binds to the immunoglobulin Jk recombination signal sequence. The IGKJRB gene is highly conserved among many species such as human, Xenopus, and Drosophila. Using cDNA fragments of the mouse Igkjrb gene, we isolated its human counterpart, IGKJRB. The human genome contains one functional IGKJRB gene and two types of processed pseudogenes. In situ chromosome hybridization analysis demonstrated that the functional gene is localized at chromosome 3q25, and the pseudogenes (IGKJRBP1 and IGKJRBP2, respectively) are located at chromosomes 9p13 and 9q13. The functional gene is composed of 13 exons spanning at least 67 kb. Three types of cDNA with different 5 sequences were isolated by rapid amplification of cDNA ends, suggesting, the presence of three proteins. The aPCR-1 protein, which possessed the exon 1 sequence, was the counterpart of the mouse RBP-2 type protein. The ...
α-globin-like genes on chromosome 16 β-globin-like genes on chromosome α-Gene family: contains a- two genes for the α-globin chains b-The ζ-gene which is expressed. c- other globin-like genes that are not expressed (pseudogenes). α-globin-like genes on chromosome 16 β-globin-like genes on chromosome α-Gene family: contains a- two genes for the α-globin chains b-The ζ-gene which is expressed. c- other globin-like genes that are not expressed (pseudogenes). Organization of the globin genes
Study Rationale: Mutations in the GBA gene are the most common genetic cause of Parkinson s disease. This gene has a nearby pseudogene, which is a genetic material that is very similar to the original gene but does not encode a protein. Because of the presence of the pseudogene, it is often difficult to identify mutations in the gene using traditional mutation detection techniques. Furthermore, specific mutations that occur as a result of a recombination between the gene and the pseudogene are often missed by the traditional genetic methods.. Hypothesis:. By using a novel technology called targeted locus amplification (TLA) we hypothesize that we will be able to better discriminate between the gene and its pseudogene, and to identify specific recombinations between GBA and its pseudogene.. Study Design:. First, we will design the TLA methods to match the target gene, GBA, and its pseudogene, and examine if it works using random DNA samples. Then, we will examine if the method works by using DNA ...
The duplicated human embryonic α-like globin genes encode a 5′ functional zeta (ζ2) gene and a highly homologous pseudogene (ψζ1). We have identified chromosomes with a ζ2-ζ1 rather than a ζ2-ψζ1 arrangement by genomic mapping and oligonucleotide analysis. The DNA sequence of a cloned downstream ζ-like gene provides direct evidence for the conversion of a ψζ1→ζ1 gene, by a ζ2 gene. We present data suggesting that this gene conversion, which removed the only identifiable inactivating mutation in the ψζ1 gene, was an interchromosomal event. The ζ2-ζ1 arrangement is common in all eight populations studied representing a previously undescribed type of polymorphism between individuals. Stable mRNA transcripts from the converted gene are absent at 16-20 weeks of gestation when transcripts from the ζ2 gene are readily detectable. © 1985.
Monell researchers have found that as much as 30 percent of the large array of human olfactory receptor differs between any two individuals.
RBMY2EP (RNA binding motif protein Y-linked family 2 member E, pseudogene), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
VENTX Full-Length MS Protein Standard (NP_055283), Labeled with [U- 13C6, 15N4]-L-Arginine and [U- 13C6, 15N2]-L-Lysine, was produced in human 293 cells (HEK293) with fully chemically defined cell culture medium to obtain incorporation efficiency at Creative-Proteomics. This gene encodes a member of the Vent family of homeodomain proteins. The encoded protein may function as a transcriptional repressor and be involved in mesodermal patterning and hemopoietic stem cell maintenance. Multiple pseudogenes exist for this gene. A transcribed pseudogene located on chromosome X may lead to antigen production in certain melanomas.
TDGF1P2 (teratocarcinoma-derived growth factor 1 pseudogene 2), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
DNA Transposons. pseudogenes. However, there is also a large amount of sequence that does not fall under any known classification.. Much of this sequence may be an evolutionary artifact that serves no present-day purpose, and these regions are sometimes collectively referred to as junk DNA. There are, however, a variety of emerging indications that many sequences within are likely to function in ways that are not fully understood. Recent experiments using microarrays have revealed that a substantial fraction of non-genic DNA is in fact transcribed into RNA,[6] which leads to the possibility that the resulting transcripts may have some unknown function. Also, the evolutionary conservation across the mammalian genomes of much more sequence than can be explained by protein-coding regions indicates that many, and perhaps most, functional elements in the genome remain unknown.[7] The investigation of the vast quantity of sequence information in the human genome whose function remains unknown is ...
Also in great numbers are transposons. About a third of the genome are Gypsy-type retrotransposons. Several other classes of transposons are present also. In the end, just over a quarter (26%) of the genome is non-repetitive. While these transposons do not themselves appear to contain phytopathological genes, their presence appears to be driving expansion of some key families of such genes. Comparison of genomic scaffolds with the other two sequenced Phytophora show striking overall conservation of conserved genes, but with local rearrangements and expansion of the zones between conserved genes (Figure 1 plus S18 and S19). Continuing evolutionary activity in this space is shown by the fact that some of these genes are apparently inactivated but have only small numbers of mutations, suggesting very recent conversion to pseudogenes. A transposon polymorphism was also found -- an insertion in one haplotype which is absent in another (figure S9 ...
FUNCTION: This gene encodes a scaffolding molecule that regulates the actin cytoskeleton. The protein directly interacts with filamentous actin and a variety of cell membrane proteins through multiple actin binding sites, SH3 domains, and a proline-rich region containing binding sites for SH3 domains. The cytoplasmic protein localizes to membrane ruffles, lipid rafts, and the leading edges of cells. It is implicated in dynamic actin remodeling and membrane trafficking that occurs during receptor endocytosis and cytokinesis. The mouse genome contains at least two pseudogenes located on chromosomes 9 and 17. [provided by RefSeq, Jul 2008 ...
From NCBI Gene:. This gene encodes a member of the endophilin family of Src homology 3 domain-containing proteins. The encoded protein is involved in endocytosis and may also play a role in the cell cycle. Overexpression of this gene may play a role in leukemogenesis, and the encoded protein has been implicated in acute myeloid leukemia as a fusion partner of the myeloid-lymphoid leukemia protein. Pseudogenes of this gene are located on the long arm of chromosomes 11 and 17. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]. From UniProt: ...
This gene encodes an RNA-binding protein that is involved in growth regulation. This protein is present in pre-ribosomal ribonucleoprotein complexes and may be involved in ribosome assembly and the regulation of intermediate and late steps of rRNA processing. This protein can interact with the cytoplasmic domain of the ErbB3 receptor and may contribute to transducing growth regulatory signals. This protein is also a transcriptional co-repressor of androgen receptor-regulated genes and other cell cycle regulatory genes through its interactions with histone deacetylases. This protein has been implicated in growth inhibition and the induction of differentiation of human cancer cells. Six pseudogenes, located on chromosomes 3, 6, 9, 18, 20 and X, have been identified ...
Gene target information for LOC340089 - POM121 membrane glycoprotein (rat) pseudogene (human). Find diseases associated with this biological target and compounds tested against it in bioassay experiments.
In the beginning I was also advised not to use TE buffer, but now I just do it with TE and never had problems, but in theory I think that it can give problems because of the neutralizing effect of the EDTA. I know someone here that uses TE, but with a 10x diluted concentration EDTA ...
Pseudogenes resulting from the retrotransposition of an RNA intermediate are known as processed pseudogenes; pseudogenes that ... into protein-coding sequences and a substantial number of pseudogenes are actively transcribed. Because pseudogenes are ... Pseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer ... Pseudogene sequences appear to accumulate mutations more rapidly than coding sequences due to a loss of selective pressure. ...
Few NUMT pseudogenes associated with diseases are found within exons or at the exon-intron boundaries of human genes. For ... For instance, a large NUMT pseudogene was found on chromosome 1, while more recent analysis of the same sequence led to a ... 2009). "Mitochondrial Pseudogenes in the Nuclear Genome of Aedes Aegypti Mosquitoes: Implications for the past and Future ... In addition, De novo integration of NUMT pseudogenes into the nuclear genome has an adverse effect in some cases, promoting ...
However, some pseudogenes have been found to be conserved in mammals. The simplest explanation for this is that these noncoding ... Other pseudogenes have also been found to be conserved between humans and mice and between humans and chimpanzees, originating ... Nov 2010). "Pseudogenes and Their Evolution". eLS. Nishikimi M, Kawai T, Yagi K (October 1992). "Guinea pigs possess a highly ... Pseudogenes commonly emerge following a gene duplication or polyploidization event. With two functional copies of a gene, there ...
SINEs however should not be mistaken as RNA pseudogenes. In general, pseudogenes are generated when processed mRNAs of protein- ... These pseudogenes, though non-functional may in some cases still possess promoters, CpG islands, and other features which ... Thus SINEs can be playing a vital role in the generation of pseudogenes, which themselves are known to be involved in ... Vanin EF (1985). "Processed pseudogenes: characteristics and evolution". Annual Review of Genetics. 19: 253-72. doi:10.1146/ ...
Additionally, pseudogenes may be functional; 67% of human OR pseudogenes are expressed in the main olfactory epithelium, where ... Phantosmia Receptor Trace amine-associated receptor Odorant Pseudogenes Gene family Gaillard I, Rouquier S, Giorgi D (February ... species with higher pseudogene count would also have a decreased olfactory ability. This assumption is flawed. Dogs, which are ... and the remaining 600 candidates are pseudogenes. The reason for the large number of different odor receptors is to provide a ...
This gene has multiple pseudogenes. GRCh38: Ensembl release 89: ENSG00000135390 - Ensembl, May 2017 "Human PubMed Reference:". ...
Different types of pseudogenes exist. Non-processed pseudogenes are genes that acquired mutations over time becoming non- ... Pseudogenes that have become isolated from the gene family they originated in, are referred to as orphans. Gene families arose ... Processed pseudogenes are genes that have lost their function after being moved around the genome by retrotransposition. ... Gene loss may be the deletion of genes or the complete loss of function, becoming pseudogenes. In addition to classification by ...
This gene has multiple pseudogenes. BTF3 has been shown to interact with CSNK2B. GRCh38: Ensembl release 89: ENSG00000145741 - ...
This gene has multiple pseudogenes. Several alternatively spliced transcript variants have been observed, but their biological ... "Structure of gene and pseudogenes of human apoferritin H". Nucleic Acids Research. 14 (2): 721-36. doi:10.1093/nar/14.2.721. ...
Pseudogenes, also known as noncoding DNA, are extra DNA in a genome that do not get transcribed into RNA to synthesize proteins ... A pseudogene can be produced when a coding gene accumulates mutations that prevent it from being transcribed, making it non- ... Non-functional pseudogenes may be passed on to later species, thereby labeling the later species as descended from the earlier ... Genetic fragments such as pseudogenes, regions of DNA that are orthologous to a gene in a related organism, but are no longer ...
This gene has multiple pseudogenes. It is abnormally expressed in fetuses of both IVF and ICSI, which may contribute to the ...
Imai K, Nakamura M, Yamada M, Asano A, Yokoyama S, Tsuji S, Ginns EI (1994). "A novel transcript from a pseudogene for human ... Glucosidase, beta; acid, pseudogene, also known as GBAP, is a human gene. GRCh38: Ensembl release 89: ENSG00000160766 - Ensembl ... Martínez-Arias R, Calafell F, Mateu E, Comas D, Andrés A, Bertranpetit J (2001). "Sequence variability of a human pseudogene". ... Sorge J, Gross E, West C, Beutler E (1990). "High level transcription of the glucocerebrosidase pseudogene in normal subjects ...
... such nonfunctional genes are called pseudogenes. "Orphan" genes, whose sequence shows no similarity to existing genes, are less ... redundancy Genetic algorithm Haplotype List of gene prediction software List of notable genes Predictive medicine Pseudogene ...
Neighboring genes of C17orf53 are that of RNU6-131, RNA U6 Small Nuclear 131 Pseudogene, and ASB16, Ankyrin Repeat And SOCS Box ... "RNU6-131P Gene - GeneCards , RNU6-131P Pseudogene". www.genecards.org. Retrieved 2018-05-06. Database, GeneCards Human Gene. " ...
"Beware the pseudo gene genies". The Guardian. 19 July 2015.. *^ a b Ledford H (2008). "Disputed definitions". Nature. 455 (7216 ... "Beware the pseudo gene genies". The Guardian.. *^ a b c Moore, David S. (2015). The Developing Genome: An Introduction to ...
UBE2L3, UBE2L6; (UBE2L1, UBE2L2, UBE2L4 are pseudogenes). *UBE2M. *UBE2N. *UBE2O. *UBE2Q1, UBE2Q2 ...
Within the genome are also six pseudogenes. The genome contains 250 genes involved in fatty acid metabolism, with 39 of these ...
OR pseudogenes in their cluster. Some adult tooth whales express 77% OR pseudogenes and are completely devoid of olfactory ... Pseudogenes are also subject to genomic drift, since they are rendered as non-functional and are believed to evolve in a ... More than 900 human OR genes and pseudogenes have been identified. Close to 63% of the ORs are changed by a random process of ... After this duplication event, one of the two genes may mutate and disable its function, rendering it as a pseudogene. ...
So, in fact, pseudogenes can act as sources of sequence variants which can be transferred to functional genes in novel ... The pseudogene-templated changes might eventually become fixed as long as they did not possess deleterious effects. ... In contrast, it is possible that pseudogenes could serve as templates. During the course of evolution, functional source genes ... While comparing the homologous genes of human SIGLEC11 and its pseudogene in the chimpanzee, bonobo, gorilla and orangutan, it ...
Li WH, Gojobori T, Nei M (1981). "Pseudogenes as a paradigm of neutral evolution". Nature. 292 (5820): 237-239. Bibcode: ...
There are approximately 10 to 14 copies of this gene including the pseudogenes scattered across the human genome, among which ... Freytag SO, Bock HG, Beaudet AL, O'Brien WE (1984). "Molecular structures of human argininosuccinate synthetase pseudogenes. ...
Balakirev ES, Ayala FJ (2003). "Pseudogenes: are they "junk" or functional DNA?". Annual Review of Genetics. 37 (1): 123-51. ... and pseudogenes, nonfunctional DNA sequences that originated from functional genes. The share of the human genome that may be ...
... such as a reduced count of CpG islands in pseudogenes, or the differences in G-C content between pseudogenes and their ... Pseudogenes are close relatives of genes, sharing very high sequence homology, but being unable to code for the same protein ... Pseudogene prediction utilises existing sequence similarity and ab initio methods, whilst adding additional filtering and ... Signal sensors also can be honed to pseudogenes, looking for the absence of introns or polyadenine tails. Metagenomics is the ...
There are multiple pseudogenes for this gene. Alternative splicing results in multiple transcript variants. The COX20 gene is ...
Li, W. H.; Gojobori, T.; Nei, M. (1981). "Pseudogenes as a paradigm of neutral evolution". Nature. 292 (5820): 237-9. Bibcode: ...
Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M (2010). "Identification and analysis of unitary pseudogenes: historic and ... see Unitary pseudogenes) and the cofactor FAD+. This reaction produces 2-oxogulonolactone (2-keto-gulonolactone), which ...
... now called pseudogenes). This prediction was shown to be correct when many multigene families and pseudogenes were discovered ... Li, W. H.; Gojobori, T.; Nei, M. (1981). "Pseudogenes as a paradigm of neutral evolution". Nature. 292 (5820): 237-239. Bibcode ...
Pseudogenes of this gene have been characterized. GRCh38: Ensembl release 89: ENSG00000136888 - Ensembl, May 2017 GRCm38: ...
However, this can also lead to complete loss of gene function and thus pseudo-genes. More commonly, single amino acid changes ... September 2014). "Comparative analysis of pseudogenes across three phyla". Proceedings of the National Academy of Sciences of ...
We analyzed the occurrences of conserved protein patterns in the intergenic region of yeast, worm, fruitfly and human chromosomes 21 and 22. We found that 67 pseudomotif p atterns are over-represented in the fly genome, and 34, in the worm. Among the over-represented patterns are the well-known Zinc finger, leucine zipper, and nucleotide-bin ding motif. We argue that the enrichment of these patterns in the intergenic region reflects the fact that some of them are remaining fragments of ancient disabled protein -coding genes. ...
Pseudogenes ornaticeps is a species of beetle in the family Cerambycidae, and the only species in the genus Pseudogenes. It was ...
Homologous Processed Pseudogenes database rel 4.0) Hoppsigen is a nucleic database of homologous processed pseudogenes. The ... Processed pseudogenes identification. Processed pseudogenes were identified by looking in complete genomes of mouse and human ... What is a processed pseudogene?. Processed pseudogenes are retroelements (like SINE and LINE). They are generated by two ways: ... Duplication of an existing processed pseudogene in germ line cells.. So if we compare processed pseudogenes to their functional ...
... and new research suggests pseudogenes have a function, further discrediting the junk DNA argument ... Regarding your comments on pseudogenes, a recent publication in Nature1 posits that pseudogene mRNA may be used as a decoy to ... Methane, ethane, and pseudogene functions. Published: 9 October 2010 (GMT+10). Image: wikipedia. There is too much methane in ... Here is one comment made by one of my colleagues: "Hi Rob-Thanks! The new paper on pseudogenes is very important because we ...
... Human pseudo gene TUBA4B. Represented by 15 ESTs from 13 cDNA libraries. Corresponds ...
In this review we discuss the latest developments in pseudogene research, focusing on how pseudogenes impact tumorigenesis ... Like other types of lncRNAs, pseudogenes can also function as master regulators for gene expression and thus, they can play a ... Given the high sequence homology with the corresponding parent genes, we also discuss challenges for pseudogene research. ... However, increasing evidence points the important role of pseudogenes in diverse cellular functions, and dysregulation of ...
Pseudogene interaction database, miRNA-pseudogene and protein-pseudogene interaction maps database Yale University pseudogene ... The PTEN pseudogene, PTENP1 is a processed pseudogene that is very similar in its genetic sequence to the wild-type gene. ... Similarly, pseudogenes are sometimes annotated as genes in genome sequences. Processed pseudogenes often pose a problem for ... Perhaps the earliest definitive example of such a pseudogene involved in cancer is the pseudogene of BRAF. The BRAF gene is a ...
RN7SKP30 RN7SK pseudogene 30 [Homo sapiens] RN7SKP30 RN7SK pseudogene 30 [Homo sapiens]. Gene ID:106479108 ... RN7SK pseudogene 30provided by HGNC. Primary source. HGNC:HGNC:45754 See related. Ensembl:ENSG00000223305 Gene type. pseudo. ... RN7SKP30 RN7SK pseudogene 30 [ Homo sapiens (human) ] Gene ID: 106479108, updated on 18-Aug-2020 ...
The presence of similar eta globin pseudogenes in humans and chimps has been used as an argument for common ancestry of the two ... Pseudogenes are DNA sequences that resemble functional genes but seem to have no purpose. ... Two types of pseudogenes are known: unprocessed pseudogenes and processed pseudogenes. Processed pseudogenes are so named ... The possibility that pseudogenes may have some function is worth exploring further. Some pseudogenes are believed to function ...
Pseudogenes were once thought to be genomic fossils-the broken remnants of genes that mutated long ago. However, research is ... Now, a new fruit fly study showed that it occurs in an olfactory receptor pseudogene once thought to be a broken gene.1 In fact ... Pseudogenes were originally characterized as the remnants of once-functional genes. This was based on the apparent stop ... Olfactory receptor pseudo-pseudogenes. Nature. 539 (7627): 93-97.. * Dabrowski, M., et al. 2015. Translational readthrough ...
Recent discoveries of function in certain pseudogenes have led to the recognition, by some evolutionists, of widespread ... pseudogenes, the urate oxidase (Uox) pseudogenes and the GULO pseudogenes. Max4 has included all the foregoing as exemplary ... While inferred pseudogenes do tend to have KA/KS higher than those of genes, most of the values for pseudogenes are well under ... are necessarily incompatible with pseudogene function:. How pervasive are "functional" pseudogenes? Many pseudogenes have been ...
To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a ... Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the ... We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one ... Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily ...
Törnquist K., Kemppainen K. (2018) Transient Receptor Potential Cation Channel, Subfamily C, Member 2, Pseudogene. In: Choi S ...
Providing a list of methods useful both to those who wish to study pseudogenes and to those who actually want to avoid their ... inadvertent detection, Pseudogenes: Functions and Protocols explores techni ... this thorough volume delves into methods for pseudogene identification, for the detection of pseudogene transcription and ... Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation Florian A. Karreth, Ugo Ala, Paolo Provero, Pier ...
Pseudogene), Ribosomal Protein L24 Pseudogene 6, including: function, proteins, disorders, pathways, orthologs, and expression ... Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. (PMID: 19123937) Balasubramanian S ...
Pseudogene), WEE1 Homolog (S. Pombe) Pseudogene, including: function, proteins, disorders, pathways, orthologs, and expression ...
Pseudogene), ST13, Hsp70 Interacting Protein Pseudogene 3, including: function, proteins, disorders, pathways, orthologs, and ... ST13, Hsp70 Interacting Protein Pseudogene 3 2 3 5 * Suppression Of Tumorigenicity 13 (Colon Carcinoma) (Hsp70 Interacting ...
Pseudogene), , including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene ...
Pseudogene), RNA, Ro-Associated Y4 Pseudogene 5, including: function, proteins, disorders, pathways, orthologs, and expression ... RNY4P5 (RNA, Ro-Associated Y4 Pseudogene 5) is a Pseudogene, and is affiliated with the Y RNA class. ...
Pseudogene), Adenylate Kinase 6 Pseudogene 1, including: function, proteins, disorders, pathways, orthologs, and expression. ...
Pseudogene), RNA, 7SK Small Nuclear Pseudogene 103, including: function, proteins, disorders, pathways, orthologs, and ... RN7SKP103 (RNA, 7SK Small Nuclear Pseudogene 103) is a Pseudogene, and is affiliated with the 7SK RNA class. ...
Pseudogene), Protein Geranylgeranyltransferase Type I Subunit Beta Pseudogene 1, including: function, proteins, disorders, ... PGGT1BP1 (Protein Geranylgeranyltransferase Type I Subunit Beta Pseudogene 1) is a Pseudogene. ... Protein Geranylgeranyltransferase Type I Subunit Beta Pseudogene 1 2 3 5 * Protein Geranylgeranyltransferase Type I, Beta ...
Pseudogene), Putative Uncharacterized Protein FLJ45355, including: function, proteins, disorders, pathways, orthologs, and ...
... "the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, ... Venema claims pseudogenes are "nonfunctional." (p. 34) The problem with his argument from pseudogenes is that there is now good ... But a 2012 paper in RNA Biology notes that "pseudogenes were long considered as junk genomic DNA" but "pseudogene regulation is ... Having said that, shared pseudogenes would be best explained by common ancestry if (a) pseudogenes are truly non-functional and ...
PRKY protein kinase Y-linked (pseudogene) [Homo sapiens] PRKY protein kinase Y-linked (pseudogene) [Homo sapiens]. Gene ID:5616 ... protein kinase Y-linked (pseudogene)provided by HGNC. Primary source. HGNC:HGNC:9444 See related. Ensembl:ENSG00000099725 MIM: ... FISH localization of the human Y-homolog of protein kinase PRKX (PRKY) to Yp11.2 and two pseudogenes to 15q26 and Xq12--,q13. ... The gene is classified as a transcribed pseudogene because it has lost a coding exon that results in all transcripts being ...
The porA pseudogene was identified in all isolates. The pseudogene comprised 12 (5.5%), of which 10 were located in the ... The porA pseudogene of Neisseria gonorrhoeae- low level of genetic polymorphism and a few, mainly identical, inactivating ... Unemo M, Norlén O, Fredlund H. The porA pseudogene of Neisseria gonorrhoeae- low level of genetic polymorphism and a few, ... However, a porA pseudogene has been identified in N. gonorrhoeae. The present study investigated the prevalence and genetic ...
Adra, C.N., Ellis, N.A., McBurney, M.W. (1988) The family of mouse phosphoglycerate kinase genes and pseudogenes. Somat. Cell ... Zehavi-Feferman, R., Cooper, D.W. (1994). Estimation of the age of a phosphoglycerate kinase pseudogene in a marsupial. In ... Van Daal, A., Cooper, D.W., Molloy, P.L. (1989). A marsupial phosphoglycerate kinase (PGK) processed pseudogene. Genomics 5: ... and it is suggested that the propensity of PGK1 to form pseudogenes is an ancient (∼130 MYR BP) characteristic of mammals. The ...
On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA" Proc Natl Acad Sci U S A. ... We focus in this paper on pseudogenes and dispersed repetitive elements, since their current names reflect the prevalent view ...
"Functional Pseudogenes Are Everywhere!" by Fazale Rana (article). *"High Levels of Pseudogene Expression Help Silence the Case ... "Unitary Pseudogenes Have Function! Part 1" by Fazale Rana (article). *"Unitary Pseudogenes Have Function! Part 2" by Fazale ... Based on the data, it looks like proper expression levels of the FAAH gene require an intact FAAH pseudogene. This is not the ... There are a number of gene-pseudogene pairs in which both must be intact and transcribed for the gene to be expressed properly ...
View mouse Gm2495 Chr9:92612512-92612977 with: sequences, polymorphisms, references
  • Pseudogenes are usually identified when genome sequence analysis finds gene-like sequences that lack regulatory sequences needed for transcription or translation, or whose coding sequences are obviously defective due to frameshifts or premature stop codons. (wikipedia.org)
  • Pseudogene sequences may be transcribed into RNA at low levels, due to promoter elements inherited from the ancestral gene or arising by new mutations. (wikipedia.org)
  • Homology is implied by sequence identity between the DNA sequences of the pseudogene and parent gene. (wikipedia.org)
  • For example, amplification of a gene by PCR may simultaneously amplify a pseudogene that shares similar sequences. (wikipedia.org)
  • Similarly, pseudogenes are sometimes annotated as genes in genome sequences. (wikipedia.org)
  • Processed pseudogenes were identified by looking in complete genomes of mouse and human for sequences similar to genes with introns. (univ-lyon1.fr)
  • Then within these retroelements, we have detected non functional sequences and we have annotated them as processed pseudogenes. (univ-lyon1.fr)
  • Pseudogenes are DNA sequences that resemble functional genes but seem to have no purpose. (grisda.org)
  • The argument has two parts: that the pseudogene sequences actually have no function, and that God would not create similar non-functional sequences in humans and chimps. (grisda.org)
  • Possible function is suggested by the location of the pseudogene and differences in the extent of divergence of "intronic" and "exonic" sequences. (grisda.org)
  • However, there is much about the operation of the genome in general, and pseudogene sequences in particular, that is not well understood. (grisda.org)
  • One of the most difficult examples for creationists to explain is probably the existence of certain DNA sequences known as pseudogenes. (grisda.org)
  • Pseudogenes are DNA sequences that appear similar to functional genes, but contain important defects that appear to make them incapable of producing a functioning protein (Proudfoot 1980). (grisda.org)
  • Processed pseudogenes may be complete copies of the coding sequence, or may be incomplete copies, or may have additional inserted sequences. (grisda.org)
  • The pseudogene comprised 12 (5.5%), of which 10 were located in the promoter spacer, and 11 (1.0%) polymorphic nucleotide sites in the upstream segment containing the promoter region, i.e. the putative -10 and -35 sequences and the promoter spacer in-between, and the hypothetical PorA coding sequence, respectively. (ingentaconnect.com)
  • We focus in this paper on pseudogenes and dispersed repetitive elements, since their current names reflect the prevalent view that they constitute dispensable genomic noise (trash), rather than a vast repertoire of sequences with the capacity to shape an organism during evolution. (nih.gov)
  • Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events. (prolekare.cz)
  • Alignment of human pseudogenes with their corresponding chimpanzee sequences. (jimmunol.org)
  • For instance, DNA sequences being pseudogenes in the sense that they are not translated, may still be transcribed and the thereby produced RNA may be functional. (biomedcentral.com)
  • A variety of pseudogene annotations from multiple sources were pooled and filtered to obtain a subset of sequences that have significant mid-sequence disablements (frameshifts and premature stop codons), and that have clear evidence of full-length mRNA transcription. (biomedcentral.com)
  • Through evolutionary analysis, we have identified candidate sequences for functional human transcribed pseudogenes, and have pinpointed 68 strong candidates for further investigation as potentially functional transcribed pseudogenes across multiple mammal species. (biomedcentral.com)
  • Compared to 246 full-length P450s in Arabidopsis and 26 identifiable pseudogenes, the rice genome contains 328 full-length P450 genes and 99 designated pseudogenes with 28 partial P450 sequences that may represent 24 additional genes and/or pseudogenes. (plantphysiol.org)
  • We have previously cloned a functional cdc2 gene from Picea abies and found it to be part of a family of related sequences, largely consisting of pseudogenes. (deepdyve.com)
  • We now report on the isolation of partial cdc2 pseudogenes from Picea engelmannii and Picea sitchensis, as well as partial functional cdc2 sequences from P. engelmannii, P. sitchensis and Pinus contorta. (deepdyve.com)
  • Phylogenetic analyses of pseudogene and functional cdc2 sequences, as well as the presence of shared insertions or deletions, support the division of most of the cdc2 pseudogenes into two subfamilies. (deepdyve.com)
  • of a family of related sequences, largely consisting of pseudogenes. (deepdyve.com)
  • The pseudogene was characteristic of previously described retroelements, in that it lacks introns and is flanked by repeat sequences. (unl.edu)
  • Pseudogenes are DNA sequences that resemble protein-coding genes but they are not transcribed to a messenger RNA (mRNA) in a way that could then be translated into some functional protein. (wasdarwinright.com)
  • Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. (semanticscholar.org)
  • Structural repertoire in VH pseudogenes of immunoglobulins: comparison with human germline genes and human amino acid sequences. (semanticscholar.org)
  • The XLR sequence family: dispersion on the X and Y chromosomes of a large set of closely related sequences, most of which are pseudogenes. (semanticscholar.org)
  • Unprocessed pseudogenes are usually found in clusters of similar functional sequences on the same chromosome. (0catch.com)
  • Comparison of DNA sequences from humans, chimps, and other mammals shows a great number of shared pseudogenes. (0catch.com)
  • Pseudogenes have long been considered as nonfunctional genomic sequences. (biomedcentral.com)
  • Duplicated pseudogenes have intron-exon-like genomic structures and may still maintain the upstream regulatory sequences of their parents. (biomedcentral.com)
  • The human pseudogene is missing the promoter and all of the regulatory sequences. (blogspot.ca)
  • Pseudogenes have been found to constitute the majority of intron sequences. (biotecharticles.com)
  • Characteristics of traditional pseudogenes a. may not have promoter sequences b. have mutations which disable the function of gene c. lost splice sites and hence cannot remove introns during transcription. (biotecharticles.com)
  • These pseudogenes do not contain any intron sequences since the parent mRNA is devoid of complementary sequences for introns. (biotecharticles.com)
  • Direct repeats" are associated with movable genetic elements, which may in some cases play a role in inserting a pseudogene into a chromosome. (grisda.org)
  • The human gene is nonfunctional giving rise to a unitary pseudogene located on chromosome 8 at p21. (blogspot.com)
  • A pseudogene on chromosome 21q22.1 that encodes a keratin-associated protein of unknown function. (thefreedictionary.com)
  • A pseudogene on chromosome 14q13.2 that encodes a member of the septin family of GTP-binding proteins, which are required for cytokinesis, membrane dynamics, vesicle trafficking, apoptosis and cytoskeleton remodelling. (thefreedictionary.com)
  • The ATP-binding cassette transporter ABCC6 gene is located on chromosome 16 between its two pseudogenes ( ABCC6P1 and ABCC6P2 ). (biomedcentral.com)
  • ABCC6 is located on chromosome 16p13 between its two pseudogenes, ABCC6P1 and ABCC6P2 , at a distance of 2.3 Mb and 1.3 Mb, respectively. (biomedcentral.com)
  • Fluorescence in situ hybridization with PAC DNA clones localized ATP1B3 to the q22 → 23 region of Chromosome (Chr) 3, and the β3 pseudogene to the p13 → 15 region of Chr 2. (elsevier.com)
  • This gene is localized on chromosome 2 in the vicinity of the NAT8 gene and may represent a pseudogene of NAT8. (mybiosource.com)
  • Integrated pseudogene annotation for human chromosome 22: evidence for transcription. (gersteinlab.org)
  • Pseudogenes identified on chromosome 22. (gersteinlab.org)
  • Research done by Dr. Deyou Zheng and colleagues in 2005 provides evidence for the transcription of approximately one fifth of the pseudogenes found on human chromosome 22. (wordpress.com)
  • According to the research, there are 525 pseudogenes on human chromosome 22, and 154 of those are processed. (wordpress.com)
  • A third neurofibromatosis type 1 (NF1) pseudogene at chromosome 15q11.2. (akjournals.com)
  • Most non-bacterial genomes contain many pseudogenes, often as many as functional genes. (wikipedia.org)
  • This is not surprising, since various biological processes are expected to accidentally create pseudogenes, and there are no specialized mechanisms to remove them from genomes. (wikipedia.org)
  • Eventually pseudogenes may be deleted from their genomes by chance DNA replication or DNA repair errors, or they may accumulate so many mutational changes that they are no longer recognizable as former genes. (wikipedia.org)
  • Pseudogenes are sometimes difficult to identify and characterize in genomes, because the two requirements of homology and loss of functionality are usually implied through sequence alignments rather than biologically proven. (wikipedia.org)
  • Of course, there are many supposed "pseudogenes" in primate genomes for which we have not yet identified any function. (evolutionnews.org)
  • Pseudogenes have long been labeled as 'junk' DNA, failed copies of genes that arise during the evolution of genomes. (evolutionnews.org)
  • We found that after their initial formation, the youngest pseudogenes in Salmonella genomes have a very high likelihood of being removed by deletional processes and are eliminated too rapidly to be governed by a strictly neutral model of stochastic loss. (prolekare.cz)
  • Those few highly degraded pseudogenes that have persisted in Salmonella genomes correspond to genes with low expression levels and low connectivity in gene networks, such that their inactivation and any initial deleterious effects associated with their inactivation are buffered. (prolekare.cz)
  • The pseudogenes in bacterial genomes are continually created from ongoing mutational processes and are subject to degradation, and eventual removal, by the further accumulation of mutations. (prolekare.cz)
  • Due to the pervasive mutational bias towards deletions that has been observed across bacterial genomes [18] - [19] , the rapidly removal of pseudogenes could be caused by the random fixation of background mutations. (prolekare.cz)
  • Alternatively, pseudogenes could effect a cost and be eliminated from bacterial genomes by an adaptive process. (prolekare.cz)
  • Here, we analyze the distribution of transcribed pseudogene annotations (TPAs) in the human and mouse genomes, examine their conservation in an expanded panel of mammals (rhesus monkey, mouse, rat, dog and cow), and assess evidence for significant selection pressures. (biomedcentral.com)
  • In support of this argument, evolutionary scientists point to the fact that pseudogenes are scattered throughout the genomes of all higher species (animals and plants) and, in particular, there are many similar pseudogenes found in all primates. (wasdarwinright.com)
  • Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. (semanticscholar.org)
  • Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. (biomedcentral.com)
  • Assessment of the distribution of the relevant chemoreceptor genes in the C. jejuni genomes deposited in the National Center for Biotechnology Information (NCBI) database led to the identification of two previously unknown tlp genes and a tlp5 pseudogene. (akjournals.com)
  • New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. (plantphysiol.org)
  • We have extended MAKER for better performance on plant genomes, developing means for the annotation of pseudogenes and ncRNA s, and optimized its parallelization for maximal performance on large, repeat-rich plant genomes. (plantphysiol.org)
  • There are four main types of pseudogenes, all with distinct mechanisms of origin and characteristic features. (wikipedia.org)
  • Two types of pseudogenes are known: unprocessed pseudogenes and processed pseudogenes. (grisda.org)
  • There are two types of pseudogenes known as 'processed' and 'unprocessed' pseudogenes. (0catch.com)
  • Different types of pseudogenes exhibit different genomic features. (biomedcentral.com)
  • It is thought that mutations in pseudogenes are neutral, and hence free from selection. (grisda.org)
  • Having said that, shared pseudogenes would be best explained by common ancestry if (a) pseudogenes are truly non-functional and (b) other explanations like hotspot mutations can never explain these shared similarities. (evolutionnews.org)
  • In conclusion, the porA pseudogene and its few inactivating mutations are widespread in the N. gonorrhoeae population and the homology with the N. meningitidis porA gene reflects their common evolutionary origin. (ingentaconnect.com)
  • The team discovered two genetic changes: (1) mutations to the FAAH gene that reduced its expression, and (2) deletion of part of the FAAH pseudogene. (reasons.org)
  • Furthermore, the researchers learned that cancer also results if mutations occur in PTEN 's corresponding pseudogene, PTENP1 . (reasons.org)
  • Each pseudogene sequence had more than 85% identity with the sequence of the human ADP/ATP translocase cDNA derived from fibroblast mRNA, but each had mutations that precluded synthesis of a functional protein. (nih.gov)
  • New cdc2 pseudogenes appear to have been formed in Picea at a much higher rate than they have been obliterated by neutral mutations. (deepdyve.com)
  • It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. (semanticscholar.org)
  • Pseudogenes are considered genomic fossils, classically defined as genomic loci with sequence similarity to functional genes, but lacking coding potential [ 14 ],[ 15 ], often due to disruptive mutations such as frameshifts, premature stop codons and deletions. (biomedcentral.com)
  • Pseudogenes are defined as defunct genomic loci with sequence similarity to functional genes but lacking coding potential due to the presence of disruptive mutations such as frame shifts and premature stop codons [ 1 - 4 ]. (biomedcentral.com)
  • Unprocessed pseudogenes are genes which were created by duplication of functional genes and subsequently lost function after acquiring various mutations. (cureus.com)
  • Pseudogenes do not code for proteins due to nonsense, frameshift, or other mutations. (news-medical.net)
  • A gene is obviously functional if it produces a functional protein product, but these pseudogenes have interruptions or mutations that would prevent a functioning protein from forming. (wordpress.com)
  • Analysis of the replacement mutations, as compared with silent ones, indicate that they are highly clustered in complementarity determining regions, for both the functional and the pseudogenes, suggesting that all genes have been submitted to similar selective pressure, and that the pseudogene repertoire may be actively used, by recombination and/or conversion process. (mysciencework.com)
  • Pseudogenes were once thought to be genomic fossils-the broken remnants of genes that mutated long ago. (icr.org)
  • As will be demonstrated in this report, the enigma of the GULO pseudogene analyzed in the light of new genomic evidence most closely aligns with a creationist model incorporating both of these paradigms. (blogspot.com)
  • We have isolated seven ADP/ATP translocase pseudogenes from recombinant human genomic libraries. (nih.gov)
  • Pseudogenes have earlier been defined as defunct copies of genes that have lost their potential as DNA templates for functional protein products [ 3 ] and they have been considered to be genomic fossils , evolving without selective pressure. (biomedcentral.com)
  • Here, we assessed the genomic evidence for such transcribed pseudogenes of potential functional importance, in the human genome. (biomedcentral.com)
  • However, it has been suggested that a single-copy of the GAPDH pseudogene is present in the feline genome and that a GAPDH assay can therefore be used to quantify feline genomic DNA (gDNA). (uzh.ch)
  • Genomic DNA from healthy individuals from five populations, Chinese (n = 24), Middle East (n = 20), Mexicans (n = 24), Caucasians (n = 50) and Africans (n = 24), were examined for copy number variations of ABCC6 and its pseudogenes by pyrosequencing and quantitative PCR. (biomedcentral.com)
  • We have cloned and characterized the Na,K-ATPase β3 subunit gene (ATP1B3), and a β3 subunit pseudogene (ATP1B3P1), from a human PAC genomic library. (elsevier.com)
  • These features of processed pseudogenes are shared with other genomic elements commonly known as retrogenes [ 7 ]. (biomedcentral.com)
  • A majority of these (~70%), are processed pseudogenes generated by reverse transcription of mRNAs followed by random genomic integration and thus, resulting in promoter region loss. (biomedcentral.com)
  • Although, pseudogenes do not have evident molecular function, accurate annotation of these interesting genomic loci is valuable for many evolutionary and genetic studies. (biomedcentral.com)
  • Providing a list of methods useful both to those who wish to study pseudogenes and to those who actually want to avoid their inadvertent detection, Pseudogenes: Functions and Protocols explores techniques involving pseudogenic DNA, RNA, and peptides/proteins, once believed to lack any functionality, but now known to be involved in complex regulatory circuits. (springer.com)
  • After a few introductory chapters that overview the functions so far attributed to pseudogenes, this thorough volume delves into methods for pseudogene identification, for the detection of pseudogene transcription and translation, and for the study of the functions of pseudogenic RNA and proteins, as well as methods to avoid pseudogene detection when the focus of the research is their highly homologous parental counterparts. (springer.com)
  • Pseudogenes can produce functional proteins, functional RNA transcripts, and even have function if they don't produce a transcript. (evolutionnews.org)
  • For example, pseudogenes might be detrimental to the organism through energetic costs incurred by the continued transcription and translation of non-functional genes and/or through the production of proteins that are toxic to cells. (prolekare.cz)
  • We offer LOC407835 mitogen-activated protein kinase kinase 2 pseudogene Peptides and LOC407835 mitogen-activated protein kinase kinase 2 pseudogene Proteins for use in common research applications: ELISA, Protein Array, Western Blot. (novusbio.com)
  • Our LOC407835 mitogen-activated protein kinase kinase 2 pseudogene Peptides and LOC407835 mitogen-activated protein kinase kinase 2 pseudogene Proteins can be used in a variety of model species: Human. (novusbio.com)
  • Choose from our LOC407835 mitogen-activated protein kinase kinase 2 pseudogene Peptides and Proteins. (novusbio.com)
  • To further test their hypothesis, the scientists turned to pseudogenes, a group of "genetic relics" that do not encode for proteins. (medicalxpress.com)
  • Using a systematic procedure based on sequence-homology, we have comprehensively identified pseudogenes of these proteins in the human genome. (semanticscholar.org)
  • In humans, it is estimated that there are approximately 16,881 pseudogenes, compared to 20,687 genes which encode functional proteins. (cureus.com)
  • Approximately 168 pseudogenes express peptides or proteins [5] . (cureus.com)
  • Historically, many biologists have avoided ascribing functions to pseudogenes because they do not directly code for proteins. (wordpress.com)
  • Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes.Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events.Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes. (nih.gov)
  • Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes. (nih.gov)
  • Pseudogenes are nonfunctional segments of DNA that resemble functional genes. (wikipedia.org)
  • Venema claims pseudogenes are "nonfunctional. (evolutionnews.org)
  • Venema identifies seven other pseudogenes pertaining to olfactory receptors that he claims are "nonfunctional. (evolutionnews.org)
  • 1 The mutation responsible for this patient's hypoalgesia occurred in a pseudogene, a region of the genome considered nonfunctional "junk DNA. (reasons.org)
  • Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms. (pnas.org)
  • Still, pseudogenes possess the tell-tale signatures that allow molecular biologists to recognize them as genes, albeit nonfunctional ones. (reasons.org)
  • The human genome probably contains almost as many pseudogenes as protein-coding genes, since the number of predicted pseudogenes ranges from 10,000 to 20,000 [ 1 ], Pseudogenes were initially thought to be nonfunctional genes and often termed as junk DNA . (biomedcentral.com)
  • Essentially, a pseudogene is a nonfunctional copy of a protein-coding gene. (labroots.com)
  • Pseudogenes are usually regarded as the disabled copies of protein-coding genes. (answersingenesis.org)
  • Transcribed pseudogenes are copies of protein-coding genes that have accumulated indicators of coding-sequence decay (such as frameshifts and premature stop codons), but nonetheless remain transcribed. (biomedcentral.com)
  • Pseudogenes (derived from protein-coding genes) are gene copies that show signs diagnostic of protein-coding deficiency. (biomedcentral.com)
  • As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. (biomedcentral.com)
  • Pseudogenes were detected as false positives in the prediction of functional protein coding genes. (gersteinlab.org)
  • Ultimately, they discovered that pseudogenes are less conserved than protein-coding genes, but they are preserved more than the intergenic background. (wordpress.com)
  • Zheng, et al, 2005) This indicates that the protein-coding genes are more important to cellular function, but the pseudogenes are more important than the intergenic background. (wordpress.com)
  • At present, the evidence from pseudogenes fits reasonably well into an evolutionary interpretation, for those who choose to make that interpretation. (grisda.org)
  • The evolutionary storytelling of OR (olfactory receptor) genes progressively becoming pseudogenes as a consequence of the diminishing importance of olfaction in the course of primate evolution collapses in the face of recent research. (answersingenesis.org)
  • Therefore, they reason, the kinds of differences exhibited by corresponding genes and pseudogenes in different organisms (orthologs) are indicative of their prior evolutionary history. (answersingenesis.org)
  • The highly conserved N. gonorrhoeae porA pseudogene may reflect an evolutionary neutral molecular clock and may be a suitable genetic target for diagnosis of N. gonorrhoeae . (ingentaconnect.com)
  • Evolutionary biologists consider pseudogenes the dead, useless remains of once functional genes. (reasons.org)
  • This feature is again in sharp contrast to eukaryotes, in which pseudogenes often persist over evolutionary timescales and may be shared by distantly related lineages, such as rodents and primates [14] - [17] . (prolekare.cz)
  • A pseudogene without any function should evolve neutrally, i.e., evolve free of evolutionary pressure and follow random drift. (biomedcentral.com)
  • Many have suggested that pseudogenes are simply molecular fossils that illustrate and provide evidence for evolutionary history. (wasdarwinright.com)
  • It is felt by many, especially evolutionary biologists, that shared pseudogenes, which have no function in any form in different species, are examples of common ancestry. (0catch.com)
  • Regarding your comments on pseudogenes, a recent publication in Nature 1 posits that pseudogene mRNA may be used as a decoy to control the level of gene expression of the real gene. (creation.com)
  • the pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. (insdc.org)
  • This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. (medicalxpress.com)
  • Pseudogenes are introduced into the genome by reverse transcription of an mRNA that is mutated and inserted back into the DNA or by duplication and mutation of the parent gene. (labroots.com)
  • IMO any ORF that is never transcribed to mRNA can be described as a pseudogene. (biostars.org)
  • If premature stop codons can be edited out of the mRNA transcript in this manner, thereby rendering functional what is otherwise a "pseudogene", this seems to me to have profound implications regarding not only GULO, but our understanding of pseudogenes in general. (blogspot.ca)
  • The insertion caused a change in transcription, which resulted in the destabilization of the Makorin-1 mRNA, the mRNA product of the pseudogenes' homologous coding gene. (wordpress.com)
  • In other words, the gene product of the PTENP1 pseudogene operates as a decoy, which allows for the appropriate levels of PTEN messenger RNAs production. (reasons.org)
  • The new findings suggest that nature has crafted a clever tale of espionage such that thousands upon thousands of mRNAs and noncoding RNAs, together with a mysterious group of genetic relics known as pseudogenes, take part in undercover reconnaissance of cellular microRNAs, resulting in a new category of genetic elements which, when mutated, can have consequences for cancer and human disease at large. (medicalxpress.com)
  • Recent experimental evidence indicates that transcribed pseudogenes may regulate the expression of homologous genes, through antisense interference, or generation of small interfering RNAs (siRNAs). (biomedcentral.com)
  • In mouse oocytes, transcribed pseudogenes have been shown to play a significant role in the generation of small interfering RNAs (siRNAs) [ 18 , 19 ], which regulate the expression of homologous genes. (biomedcentral.com)
  • Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. (plantphysiol.org)
  • Pseudogenes can complicate molecular genetic studies. (wikipedia.org)
  • The present study investigated the prevalence and genetic polymorphism of this porA pseudogene in 87 different N. gonorrhoeae strains. (ingentaconnect.com)
  • Implicit in this argument is that pseudogenes are genetic relics that have lost their original protein-coding function which had been possessed by some ancestral creature. (wasdarwinright.com)
  • Having less or more copies of ABCC6 pseudogenes is likely to influence the expression level of these pseudogenes, and thus, may have an impact on the parent gene ABCC6 , including the genetic message, the protein level and the function of the protein. (biomedcentral.com)
  • In fact many scientists think that pseudogenes are nothing more than discarded genetic fossils of a bygone era when they did have some sort of important function. (0catch.com)
  • Whether species-specific variation in TAS2R pseudogenes is solely the result of genetic drift or whether it may have been influenced by selection due to different feeding behaviors has been an open question. (biomedcentral.com)
  • An ID-based paradigm of biology can help us understand the functions of pseudogenes, whereas a neo-Darwinian paradigm leads us to wrongly assume these genes like the GULO "pseudogene" are "broken" genetic "junk. (blogspot.ca)
  • I address several recent advances in the area of genetic research regarding pseudogene functionality chronologically, starting from one of the first discoveries of a functional pseudogene and ending with a paper from this year (2013). (wordpress.com)
  • This finding means that the PTENP1 pseudogene must be functional. (reasons.org)
  • The scientists studied the interaction between the RNA encoding for the PTEN tumor suppressor gene and its closely related pseudogene, PTENP1. (medicalxpress.com)
  • PTENP1 is a pseudogene derived from PTEN that can also bind the same miRNAs. (labroots.com)
  • In this example, the pseudogene PTENP1 is acting as a tumor suppressor. (labroots.com)
  • The presence of similar eta globin pseudogenes in humans and chimps has been used as an argument for common ancestry of the two species. (grisda.org)
  • Since that time, a large number of pseudogenes have been described in humans and a wide variety of other species. (grisda.org)
  • In their paper they state, 'It should also prompt the experimental examination of the hundreds of PTC-containing presumed pseudogenes, both within and beyond chemosensory gene families in insects, humans and other organisms. (icr.org)
  • In Adam and the Genome , which we've been considering in this series , theistic evolutionist biologist Dennis Venema argues that another piece of evidence that common design cannot explain is the presence of shared pseudogenes in humans and other organisms, such as apes. (evolutionnews.org)
  • For example, identical beta-globin pseudogenes have been found in both humans and chimpanzees and this fact has been used as an argument by Professor Kenneth Miller in his book " Only a Theory " for the common ancestry of the two species [1]. (wasdarwinright.com)
  • 11 For example, the eta-globin pseudogene, which is found in both humans and chimps, has been used as an argument for the common ancestry of the two species. (0catch.com)
  • In addition, humans carry 11 TAS2R pseudogenes, some of which display evidence for substantial diversification among species, showing lineage-specific loss of function. (biomedcentral.com)
  • 50% pseudogenes in humans. (biomedcentral.com)
  • The enzyme L-glucono-γ-lactone oxidase is required for the synthesis of vitamin C. Humans cannot make this enzyme because the gene for this enzyme is defective [see Human GULOP Pseudogene ]. (blogspot.ca)
  • However, recent researches have thrown light that these conventional pseudogenes form only a small percentage of the ~ 20000 pseudogenes found in humans. (biotecharticles.com)
  • However, recent evidence has shown that many pseudogenes have very important functions in the genome of nearly every organism, humans included. (wordpress.com)
  • Molecular biologists recognize several classes of pseudogenes. (reasons.org)
  • Unusual molecular evolution of an Adh pseudogene in Drosophila. (semanticscholar.org)
  • Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. (semanticscholar.org)
  • We found a six-pseudogene signature correlated with patients' clinical outcome via bioinformatics analyses (P ≤ 0.01), and validated it in the Repository of Molecular Brain Neoplasia Data (REMBRANDT) containing 350 cases. (biomedcentral.com)
  • At SGD, we also annotate pseudogenes to unknown. (stanford.edu)
  • This qualifier is used to annotate pseudogenes only. (insdc.org)
  • As such, it is likely to mis-annotate pseudogenes as functional genes. (nih.gov)
  • Pseudogenes ornaticeps is a species of beetle in the family Cerambycidae, and the only species in the genus Pseudogenes. (wikipedia.org)
  • The Query program allows to browse the database flat files and to select sets of homologous pseudogenes from different species according to specific criteria. (univ-lyon1.fr)
  • Not only did the researchers identify functional protein-producing pseudogenes in one specific type of fruit fly, but other species as well under a variety of odor receptor repertoires. (icr.org)
  • We have used PGK1 probes derived from two closely related species of macropodid marsupials (kangaroos and wallabies) to demonstrate the existence of a large family of pseudogenes in the tammar wallaby ( Macropus eugenii ). (springer.com)
  • This post covers another paper by Tomkins claiming that the GULO pseudogenes in various primate species are not derived from a common ancestor but instead have been deactivated independently in each lineage. (blogspot.com)
  • The main question Tomkins addresses is whether the pattern of GULO pseudogenes in various species is consistent with gene loss in an ancestral species and subsequent inheritance of a pseudogene in different lineages or whether the pattern is consistent with separate and independent loss in related species. (blogspot.com)
  • In our analysis, the sub families of the Olfactory Receptors contains only lineage specific pseudogenes, while the sub families of the Zinc Fingers contains pseudogene lineages common to several species. (biomedcentral.com)
  • In the present study, approximately 600 base pairs of the g 1 -globin pseudogene were sequenced in the four Brazilian species ( A. seniculus , A. belzebul , A. fusca and A. caraya ). (scielo.br)
  • The study also confirmed the presence of a 150-base pair Alu insertion element and a 1.8-kb deletion in the g 1 -globin pseudogene in A. fusca , features found previously in the remaining three species. (scielo.br)
  • Of course, it logically follows that similar pseudogenes that are shared by different species give evidence of common ancestry and even potential times of divergence. (0catch.com)
  • In this study, we analyzed patterns of variation at human TAS2R pseudogenes in both African and non-African populations, and compared them to those observable in nonhuman primates and archaic human species. (biomedcentral.com)
  • These pseudogenes have been found to be common in different species of animals rendering them to be classified under the same phylogenetic tree in the course of evolution. (biotecharticles.com)
  • Varesio LM, Willett JW, Fiebig A, Crosson S. A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO2 Tension. (uchicago.edu)
  • In high-throughput pseudogene identification, the most commonly identified disablements are premature stop codons and frameshifts, which almost universally prevent the translation of a functional protein product. (wikipedia.org)
  • GULO pseudogenes in these organisms possess multiple indel mutatons and premature stop codons, meaning that they are not translated into a functional protein. (evolutionnews.org)
  • Guinea pigs also possess a GULO pseudogene with premature stop codons, however, and would make a good model organism for the testing of this hypothesis. (blogspot.ca)
  • All 13 genes were pseudogenes because of the presence of internal stop codons. (akjournals.com)
  • A total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. (nih.gov)
  • Pointedly, the striking discovery of the fact that the independently-derived guinea pig and human GULO pseudogenes have an astounding 36% identical 'disablement' is, if valid, as close as one can get to a resounding disproof of the entire evolutionistic 'shared mistakes' argument. (answersingenesis.org)
  • 3 The present report extends and updates these considerations, devoting special attention to the primates' olfactory receptor (OR) pseudogenes, the urate oxidase (Uox) pseudogenes and the GULO pseudogenes. (answersingenesis.org)
  • Jonathan McLatchie thinks he has evidence that the human fetus can make vitamin C [ A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene ]. (blogspot.ca)
  • It would seem that [scientists'] claim that the GULO pseudogene is a "silver bullet" argument for evolution is highly premature. (blogspot.ca)
  • a (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. (insdc.org)
  • Collectively, these reports indicate that an unknown cohort of human transcribed pseudogenes could be potentially functional in regulation of gene transcription. (biomedcentral.com)
  • Moreover, we sought to study the transcription pattern of ABCC6 and ABCC6 pseudogenes in 39 different human tissues. (biomedcentral.com)
  • Interestingly, the total transcription level of pseudogenes, ABCC6P1 + ABCC6P2 , was higher than ABCC6 in most tissues, including liver and kidney. (biomedcentral.com)
  • Estimation of copy number variations and transcription of pseudogenes is generally difficult because of the high sequence similarity between pseudogenes and their parent genes. (biomedcentral.com)
  • In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. (biomedcentral.com)
  • In this article OR pseudogenes denote such cases that disallow the production of a functional protein, irrespective of transcription status. (biomedcentral.com)
  • These pseudogenes hence become inactive without the mechanisms for transcription and processing. (biotecharticles.com)
  • That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to produce functional final protein products. (wikipedia.org)
  • Given the high sequence homology with the corresponding parent genes, we also discuss challenges for pseudogene research. (mdpi.com)
  • If this is common practice, to refer to 'pseudogenes', i.e. genes that don't express the product they might have been expected to based on sequence similarity to a functional gene, that actually do express a product, often an ncRNA, as 'expressed pseudogenes', then perhaps SO should reflect that usage, rather than impose a perhaps artificially strict definition that pseudogenes never express any product. (stanford.edu)
  • In many other cases, it would be virtually impossible to determine whether a putative prey sequence is actually a pseudogene derived from either the predator or prey DNA. (cambridge.org)
  • Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice ( Oryza sativa ) genome using sequence information available from both the indica and japonica strains. (plantphysiol.org)
  • A dinucleotide deletion (DeltaGT) at the beginning of exon 2 that leads to a frameshift and premature stop codon is considered the signature sequence of the pseudogenes. (biomedsearch.com)
  • Extending our study of the relationship between NCF-1 and psiNCF-1 to 53 unaffected control individuals, we found that although in most (n = 44), the ratio of pseudogene (DeltaGT) to functional gene (GTGT) sequence in amplicons spanning exon 2 was 2:1, as previously observed, surprisingly, in 7 persons the ratio was 1:1, and in 2 persons the ratio was 1:2. (biomedsearch.com)
  • In contrast, processed pseudogenes, having lost their introns, contain only exonic sequence and do not retain the upstream regulatory regions. (biomedcentral.com)
  • Pseudogenes have been defined as copies of protein-encoding genes that are thought to no longer have the same functional product as their parental gene but still share significant sequence similarity [4] . (cureus.com)
  • For most organisms, a variable number of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) pseudogenes have been reported. (uzh.ch)
  • 2 Other theories include retroviruses as means of pseudogene transport between different organisms. (0catch.com)
  • So if we compare processed pseudogenes to their functional homologs, they have lost introns and they have no promoter (except for processed pseudogenes which are inserted near an existing promoter). (univ-lyon1.fr)
  • Because my genome is bacteria I don't have any introns, so every same annotation for one gene will be an extra copy - pseudogene. (biostars.org)
  • Recently, researchers discovered that the products of pseudogenes may function as biomolecular decoys , protecting the "real" gene products from breakdown.1 As it turns out, this new insight has important implications for the biology of cancer. (reasons.org)
  • Implications: The VEGFR1 pseudogene, FLT1P1, is a novel and functional regulator of VEGF signaling and its targeting could be an alternative strategy to modulate its cognate/target gene expression and downstream activity in cancer. (aacrjournals.org)
  • Though the function of these pseudogenes is not clear, the identification of the prognostic pseudogenes indicated the potential roles of pseudogenes in glioma pathogenesis and they may have clinical implications in treating glioma. (biomedcentral.com)
  • The gene is classified as a transcribed pseudogene because it has lost a coding exon that results in all transcripts being candidates for nonsense-mediated decay (NMD) and unlikely to express a protein. (nih.gov)
  • The pseudogene could consist of just one exon of the parent gene (a processed pseudogene) or it could include the whole transcript from the parent gene (an unprocessed pseudogene). (labroots.com)
  • Three pseudogene alleles with coding changes in exon 3 were identified in the mule deer samples examined. (unl.edu)
  • The human pseudogene is missing exon XI. (blogspot.ca)
  • The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes. (biomedcentral.com)
  • Functions are being ascribed to pseudogenes on a fairly regular basis in contemporary genetics literature, and some of the literature is reviewed in chronological order. (wordpress.com)
  • Now, a new fruit fly study showed that it occurs in an olfactory receptor pseudogene once thought to be a broken gene. (icr.org)
  • 2016. Olfactory receptor pseudo-pseudogenes. (icr.org)
  • To characterize inactive ORs with intact open reading frame, we have developed a probabilistic Classifier for Olfactory Receptor Pseudogenes (CORP). This algorithm is based on deviations from a functionally crucial consensus, constituting sixty highly conserved positions identified by a comparison of two evolutionarily-constrained OR repertoires (mouse and dog) with a small pseudogene fraction. (biomedcentral.com)
  • Dr Robert Carter receives some positive feedback about his article ' Splicing and dicing the genome ', and comments on new research suggesting a new function for pseudogenes have a function that further renders the 'junk DNA' explanation invalid. (creation.com)
  • A 2012 paper in Science Signaling noted that although "pseudogenes have long been dismissed as junk DNA," recent advances have established that "the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes. (evolutionnews.org)
  • However, as I've pointed out before, researchers are beginning to recognize that pseudogenes are not purposeless junk. (reasons.org)
  • The importance of functional pseudogenes (as well as other classes of junk DNA ) undermines the best argument for evolution. (reasons.org)
  • Even though many people believe that pseudogenes are "junk genes," what little research there is on this topic suggests that the transcriptionally active pseudogenes play an interesting role in cancer. (labroots.com)
  • Overall, it's clear that pseudogenes are not genome junk and are clinically relevant for cancer. (labroots.com)
  • PDF] Pseudogenes: are they "junk" or functional DNA? (semanticscholar.org)
  • Pseudogenes have been placed in the 'junk DNA' category, 'dead', non-functional by-products of evolution. (wordpress.com)
  • Iterative gene prediction and pseudogene removal improves genome annotation. (gersteinlab.org)
  • RN7SKP103 (RNA, 7SK Small Nuclear Pseudogene 103) is a Pseudogene, and is affiliated with the 7SK RNA class. (genecards.org)
  • The larval cuticle protein (Lcp) cluster in Drosophila melanogaster contains four functional genes and a closely related pseudogene. (elsevier.com)
  • The first post addressed a paper by Jeffrey Tomkins on the β-globin pseudogene [ Creationists questioning pseudogenes: the beta-globin pseudogene ]. (blogspot.com)
  • In 2011, researchers from Harvard University proposed that the competitive endogenous RNA hypothesis explains why transcribed pseudogenes are so important for gene expression. (reasons.org)
  • Because pseudogenes have long been viewed as "a paradigm of neutral evolution" [20] , this is the favored hypothesis. (prolekare.cz)
  • We found 1750 such transcribed pseudogene annotations (TPAs) in the human genome (corresponding to ~11.5% of human pseudogene annotations). (biomedcentral.com)
  • You might be able to try your method on https://www.ncbi.nlm.nih.gov/nuccore/AL450380.1 , then download its gff3 file, count the /pseudo or pseudogene annotations and compare. (biostars.org)
  • We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. (biomedcentral.com)
  • The p47-phox gene, NCF-1, has 2 nearly identical pseudogenes (psiNCF-1) in proximity at chromosomal locus 7q11.23. (biomedsearch.com)
  • We therefore hypothesized that ABCC6 pseudogenes would be liable to chromosomal rearrangements and thereby subject to copy number variations. (biomedcentral.com)
  • Like other types of lncRNAs, pseudogenes can also function as master regulators for gene expression and thus, they can play a critical role in various aspects of tumorigenesis. (mdpi.com)
  • The paper concludes that "pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression. (evolutionnews.org)
  • Adding to these earlier studies is new work indicating that pseudogenes control gene expression by acting as decoys to protect gene products from destruction. (reasons.org)
  • There are very good reasons to revise the definition of 'pseudogene' to include a wide variety of biological functions, from gene expression and cellular function to gene regulation and tumor suppression. (wordpress.com)
  • It has been proposed that identification of processed pseudogenes can help improve the accuracy of gene prediction methods. (wikipedia.org)
  • Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47 degrees chronic granulomatous disease carrier detection. (biomedsearch.com)
  • Identification of pseudogenes in the Drosophila melanogaster genome. (semanticscholar.org)
  • Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. (semanticscholar.org)
  • Identification and characterization of pseudogenes in the rice gene complement. (nih.gov)
  • I was wondering what the scientific community would expect to see with respect to how a 'pseudogene' that expresses a transcript would be annotated in SO. (stanford.edu)
  • I'm also more familiar with GO practice that SO, but it seems that if researchers still refer to a feature as a pseudogene, even after it has been discovered to produce a transcript that may function as an ncRNA, then SO should attempt to reflect the usage of the research community. (stanford.edu)
  • A total of 22,033 gene models within the Osa1 Release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, or, for genes residing within a segmentally duplicated region, lack of a paralog or significantly shorter corresponding paralog. (nih.gov)
  • Go here , and here to read a couple of articles about the biological roles of pseudogenes. (reasons.org)
  • The very fact that pseudogenes are still present and recognizable after tens of millions of years without any beneficial function just doesn't seem to make sense. (0catch.com)
  • They seem to think that pseudogenes are not compatible with the concept of Intelligent Design Creationism. (blogspot.ca)
  • This discovery was one of the first insights into the important functions of pseudogenes in gene regulation. (wordpress.com)
  • Based on the data, it looks like proper expression levels of the FAAH gene require an intact FAAH pseudogene. (reasons.org)
  • Pseudogene expression in cancer is very specific to the tissue and type of tumor, and their function varies. (labroots.com)
  • These two pseudogenes trap the miRNAs that would suppress translation of HMGA1, allowing for more expression of functional HMGA1 protein. (labroots.com)
  • Because pseudogene expression is tissue- and cancer type-specific, pseudogenes could be exploited for more targeted therapies or as a diagnostic tool. (labroots.com)
  • Pseudogene expression could even be used as a prognostic marker. (labroots.com)
  • How to determine effect of SNP on the expression of pseudogene. (biostars.org)
  • Interestingly, this pseudogene (designated as FLT1P1) was found to be transcribed bidirectionally and functionally modulated cognate VEGFR1 protein expression in the cells. (aacrjournals.org)
  • The expression pattern of ABCC6P2 in 39 human tissues was highly similar to that of ABCC6 and ABCC6P1 suggesting similar regulatory mechanisms for ABCC6 and its pseudogenes. (biomedcentral.com)
  • Few of these pseudogenes have been shown to regulate the post-transcriptional expression of genes. (news-medical.net)
  • Using a pseudogene-mining approach, we performed pseudogene expression profiling in 183 glioma samples from the Chinese Glioma Genome Atlas (CGGA) and set it as the training set. (biomedcentral.com)
  • to select the regions of the pseudogenes similar to the 5'NCR (or 3'NCR) of the functional gene. (univ-lyon1.fr)
  • It is possible that this pseudogene has not undergone deletion of GT, but more likely, based on analysis of additional NCF-1/psiNCF-1 markers, it represents the previously unidentified product of the reciprocal crossover of DNA fragments between the functional gene and one of its pseudogenes. (biomedsearch.com)
  • Analysis of BAC clones containing mule deer PRNP genes revealed a full length functional gene and a processed pseudogene. (unl.edu)
  • Here's a diagram that compares what is left of the human GULOP pseudogene with the functional gene in the rat genome. (blogspot.ca)
  • The first pseudogene was discovered in 1977 and, until very recently, pseudogenes were thought to be irrelevant byproducts of evolution scattered throughout the genome. (labroots.com)
  • In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa , a methylated 5S rRNA pseudogene, Ψ 63 , was identified. (genetics.org)
  • Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity. (uchicago.edu)
  • The newly discovered functions are making the term 'pseudogene' notoriously ambiguous. (wordpress.com)
  • This has created difficulty in defining exactly what is meant by the term pseudogene, and many have proposed a revision of the current understanding of pseudogenes. (wordpress.com)
  • Human pseudogene sets. (gersteinlab.org)
  • The human pseudogene is missing exons I to VI. (blogspot.ca)
  • Now there's a slight problem with this scenario since RNA editing requires RNA and, as far as I know, the human pseudogene isn't transcribed. (blogspot.ca)
  • The problem for Venema's argument is that researchers who study pseudogenes caution against assuming that pseudogenes are non-functional, since we're only starting to understand them. (evolutionnews.org)
  • A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. (biomedcentral.com)
  • Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection. (prolekare.cz)
  • A 630-bp fragment including the larval cuticle pseudogene locus (Lcpψ) was nucleotide sequenced in 10 strains of D. melanogaster and a 458-bp Lcpψ fragment from D. simulans was also sequenced. (elsevier.com)
  • Even if they are non-functional, orthologous primate urate oxidase (Uox) pseudogenes contain a phylogenetically-discordant, premature stop codon and a duplication. (answersingenesis.org)
  • Mitochondrial Ribosomal Protein (MRP) pseudogenes identified in Aug. 2001. (gersteinlab.org)
  • the pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. (insdc.org)