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. N1 - Funding Information: Thanks to T. Bureau, N. Juretic and D. Hoen (McGill U.) for discussions. This work was supported in part by a Discovery Grant from the National Science and Engineering Council of Canada to P.M.H., and by National Institutes of Health grant # P50 HG02357-01 to M.G. Funding to pay the Open Access publication charges for this article was provided by McGill University.. PY - 2005. Y1 - 2005. 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 ...

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: ...

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 ...

IMPROVED TECHNIQUES FOR THE IDENTIFICATION OF PSEUDOGENES. L. Coin and R. Durbin Wellcome Trust Sanger Institute. BIOINFORMATICS 2004 Presented by: Oscar Sanchez Plazas. Outline. Problem definition Previous works on pseudogene identification Proposed method Protein domain profile (Pfam)...

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] ...

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 MRPL45P1 gene (Pseudogene), Mitochondrial Ribosomal Protein L45 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.

TDGF1P5 (teratocarcinoma-derived growth factor 1 pseudogene 5), 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 ...

Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This gene is a member of the DPRX homeobox gene family. Evidence of mRNA expression has not yet been found for this gene. Multiple, related processed pseudogenes have been found which are thought to reflect expression of this gene in the germ line or embryonic cells. [provided by RefSeq, Jul 2008 ...

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 ...

GPU=1 CUDNN=1 CUDNN_HALF=0 OPENCV=1 AVX=0 OPENMP=0 LIBSO=0 # set GPU=1 and CUDNN=1 to speedup on GPU # set CUDNN_HALF=1 to further speedup 3 x times (Mixed-precision using Tensor Cores) on GPU Tesla V100, Titan V, DGX-2 # set AVX=1 and OPENMP=1 to speedup on CPU (if error occurs then set AVX=0) DEBUG=0 ARCH= -gencode arch=compute_30,code=sm_30 \ -gencode arch=compute_35,code=sm_35 \ -gencode arch=compute_50,code=[sm_50,compute_50] \ -gencode arch=compute_52,code=[sm_52,compute_52] \ -gencode arch=compute_61,code=[sm_61,compute_61] OS := $(shell uname) # Tesla V100 # ARCH= -gencode arch=compute_70,code=[sm_70,compute_70] # GTX 1080, GTX 1070, GTX 1060, GTX 1050, GTX 1030, Titan Xp, Tesla P40, Tesla P4 ARCH= -gencode arch=compute_61,code=sm_61 -gencode arch=compute_61,code=compute_61 # GP100/Tesla P100 � DGX-1 # ARCH= -gencode arch=compute_60,code=sm_60 # For Jetson TX1, Tegra X1, DRIVE CX, DRIVE PX - uncomment: # ARCH= -gencode arch=compute_53,code=[sm_53,compute_53] # For Jetson Tx2 or ...

Gene target information for FAM192BP - family with sequence similarity 192, member A pseudogene (human). Find diseases associated with this biological target and compounds tested against it in bioassay experiments.

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 ...

With just over 4 weeks to go to the Level 1 SFDR deadline and with clarity on Level 2 now published, ESG regulatory momentum is not slowing down.