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
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 ...
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... ...
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: ...
First of all, it s a misconception even among many biochemists that all proteins need to fold to be functional. In fact, the importance of disordered proteins and those with long disordered regions is now becoming more clear. Try searching the lit for intrinsically disordered proteins and you ll come up with a number of hits. These proteins (or certain domains) are unfolded and yet are perfectly functional, and in many cases are just as highly conserved as folded protein domains, though often of lower sequence complexity [1] (and hence, easier to evolve via random generation). In fact, there is evidence that disordered proteins outnumber ordered proteins, but that the ordered ones represent more resolved structures in the PDB simply because (big shock) they re easier to crystallize. So one possible way for folded proteins to come about is by evolving from functional yet disordered proteins, and in this case there would never be a period of time when there was not a selectable function. And of ...
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 ...
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 ...
... ? 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 ...
Abstract Researchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these pseudogenes are actually functional. This paper is an overview of some of the research done…
The Tgif gene family (within the TALE class) is equivalent to the TGIF gene class of Bürglin and Mukherjee (2007). The Tgif gene family includes two human genes on autosomes and one gene with homologues on the X and Y chromosomes (TGIF2LX and TGIF2LY). The autosomal genes have generated a total of five pseudogenes although some of these are short and represent partial integrants of reverse transcribed mRNA (Holland et al. 2007). Two of the pseudogenes, TGIF2P2 and TGIF2P3 are very similar neighbouring loci that must have originated by tandem duplication after a single integration event. The sex-linked gene may also have arisen by retrotransposition (Blanco-Arias et al. 2002). There is one orthologue in amphioxus, and two tandemly arranged orthologues in Drosophila (achintya, achi and vismay, vis ...
Complete information for TSPY9P gene (Pseudogene), Testis Specific Protein, Y-Linked 9, Pseudogene, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
The central dogma of molecular biology, as proposed in 1970 by Francis Crick and James Watson, holds that genetic information is transferred from DNA to functional proteins by way of messenger RNA (mRNA). This suggests that ...
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By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. It includes options to display the comprehensive GENCODE set and pseudogenes. To customize these options, the respective boxes can be checked or unchecked at the top of this description page. Our FAQ includes examples of how to display a single transcript per gene and switching between the basic and comprehensive gene sets.. This track also includes a variety of labels which identify the transcripts when visibility is set to full or pack. Gene symbols (e.g. NIPA1) are displayed by default, but additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID (uc001yve.4), UniProt Display ID (Q7RTP0) and OMIM ID (608145). Additional information about gene and transcript names can be found in our FAQ.. This track, in general, follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by ...
By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. It includes options to display the comprehensive GENCODE set and pseudogenes. To customize these options, the respective boxes can be checked or unchecked at the top of this description page. Our FAQ includes examples of how to display a single transcript per gene and switching between the basic and comprehensive gene sets.. This track also includes a variety of labels which identify the transcripts when visibility is set to full or pack. Gene symbols (e.g. NIPA1) are displayed by default, but additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID (uc001yve.4), UniProt Display ID (Q7RTP0) and OMIM ID (608145). Additional information about gene and transcript names can be found in our FAQ.. This track, in general, follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by ...
Here, we are primarily interested in modeling gene insertions/deletions with consideration for truncated genes. We have not attempted to infer the functionality of any truncated genes. First, there has never been a standard criterion in the literature for pseudogene identification (Chain et al. 2004; Lerat and Ochman 2004). Second, detection of pseudogenes requires extensive knowledge of each genes transcription and its proteins function but this is beyond the scope of this study. Finally, the boundary between gene and pseudogene might rather be ambiguous (Zheng and Gerstein 2007). Presence of an annotated gene within a genome does not necessarily suggest its functionality, but ironically, some shortened homologs might still carry out some function (Ogata et al. 2001).. Our current study classifies genes into three categories (presence/absence/fragment) and makes no attempt to examine any sequence divergence at the gene or subgenic levels. If a whole gene or a fraction of it was replaced via a ...
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. The β3 subunit gene is > 50 kb in size and is split
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 ...
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]
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
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 ...
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). ...
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 ...
... , Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
... , Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol.
OR5AS1 - OR5AS1 (untagged)-Human olfactory receptor, family 5, subfamily AS, member 1 (OR5AS1) available for purchase from OriGene - Your Gene Company.
in DNA & Cell Biology (1996), 15(12), 1009-23. A 37LRP/p40 polypeptide is of major interest because it is consistently up-regulated in cancer cells in correlation with their invasive and metastatic phenotype. Furthermore, this polypeptide presents ... [more ▼]. A 37LRP/p40 polypeptide is of major interest because it is consistently up-regulated in cancer cells in correlation with their invasive and metastatic phenotype. Furthermore, this polypeptide presents intriguing multifunctional properties because it has been characterized as the precursor of the metastasis-associated 67-kD laminin receptor (67LR) and as a cytoplasmic ribosomal-associated protein. The isolation of the 37LRP/p40 gene is a prerequisite for identifying the molecular mechanisms responsible for the constant up-regulation of the 67LR expression in cancer cells. To date, the active 37LRP/p40 gene has never been identified in any species due to the existence of multiple pseudogenes in most vertebrates genomes. In this study, we ...