• The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. (nih.gov)
  • PCR-based screening of over 500 Alu insertion loci resulted in the recovery of a few "young" Alu elements that also resided at orthologous positions in non-human primate genomes. (ojp.gov)
  • Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. (researchgate.net)
  • Alignment of HACNS4 to orthologous sequences from nonhuman genomes. (yale.edu)
  • Comparative gene mapping among human, murine, and canine genomes have the potential to rapidly identify mutations that underlie various disease syndromes. (stanford.edu)
  • Nearly 39% of Ciona GPCRs have unambiguous orthologs of vertebrate GPCR families, as defined for the human, mouse, puffer fish and chicken genomes. (biomedcentral.com)
  • With the advent of fully sequenced genomes, the computational study of orthologous protein relationships in evolution, comparative genomics, but also for substantiating the evolutionary conservation of fundamental cellular processes increased exponentially. (biomedcentral.com)
  • The chain track shows alignments of human (Dec. 2013 (GRCh38/hg38)) to other genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. (noncode.org)
  • second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. (biomedcentral.com)
  • We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. (biomedcentral.com)
  • This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts) we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. (biomedcentral.com)
  • In practice, two genes α and β are usually annotated as orthologous if their products are the "best reciprocal hits": that is, one of the proteins encoded by the α gene of species A has, as its most similar counterpart in species B, one of the proteins encoded by the β gene, and vice versa. (biomedcentral.com)
  • A region of 10 genes or less was deemed an acceptable gap between anchors, and thus variability in the gene order was allowed. (ubc.ca)
  • This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution. (nih.gov)
  • Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. (kb.se)
  • The genomic organization and regulation of the murine and human resistin genes are divergent and may explain these discrepant findings ( 13 ). (diabetesjournals.org)
  • Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. (biomedcentral.com)
  • An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. (biomedcentral.com)
  • HACNSs are disproportionately associated with genes involved in neuronal migration, adhesion, axon guidance and synapse formation, suggesting that cis-regulatory changes in human evolution may have contributed to changes in brain development and function. (yale.edu)
  • Many of these hotspot regions of CNV formation are functionally relevant, with a bias toward genes involved in immune function, some of which were previously shown to evolve under balancing selection in humans. (biomedcentral.com)
  • Genetic variants and their putative effects on microRNAseed sites: Characterization of 3' untranslated region of genes associated with temperament. (usda.gov)
  • With the advent of NGS technique, the explosion of NGS data generated from the tumor tissues help researchers identify driver mutations in cancer-related genes, but relatively less attention is paid to the SNP data in healthy human populations when studying cancer. (biomedcentral.com)
  • By simply dividing the human genes into cancer-related genes and other genes, we compared the features of nonsynonymous, synonymous and nonsense mutations in these two gene sets from multiple aspects. (biomedcentral.com)
  • The synonymous SNPs, after excluding those in splicing regions, exhibit preferred changes in codon usage and higher codon frequencies in cancer-related genes compared to other genes, indicating the constraint exerted on these mutations. (biomedcentral.com)
  • Mammalian β-globin loci are composed of multiple orthologous genes whose expression is erythroid specific and developmentally regulated. (wustl.edu)
  • The expression of these genes both from the endogenous locus and from transgenes is strongly influenced by a linked 15-kilobase region of clustered DNaseI hypersensitive sites (HSs) known as the locus control region (LCR). (wustl.edu)
  • and protein localization to chromosome, centromeric region. (nih.gov)
  • COL7A1 is located on the short arm of human chromosome 3, in the chromosomal region denoted 3p21.31. (wikipedia.org)
  • The Mcs7 region on rat chromosome 10 (RNO10) is orthologous to human 17q, a common site of genetic aberrations in breast cancer. (mcw.edu)
  • GARDINER, K. J. Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions. (bvsalud.org)
  • Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. (embl.de)
  • The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. (biomedcentral.com)
  • Collagen alpha-1(VII) chain is a protein that in humans is encoded by the COL7A1 gene. (wikipedia.org)
  • Sequence alignment and analysis of orthologous proteins to human bactericidal/permeability-increasing protein (huBPI). (elifesciences.org)
  • Sequence alignment and analysis of orthologous Actinopterygii bactericidal/permeability-increasing protein (BPI). (elifesciences.org)
  • Bactericidal/permeability-increasing protein-anti-neutrophil cytoplasmic antibodies (BPI-ANCA) from people with cystic fibrosis (PwCF) do not recognize orthologous proteins of human BPI (huBPI). (elifesciences.org)
  • We present evidence for the de novo origin of the Wookiee wookiee protein-coding gene GLABR since their divergence from humans. (ubc.ca)
  • Orthologous to human NOTUM (notum, palmitoleoyl-protein carboxylesterase). (zfin.org)
  • The mature miRNA is then loaded onto an Argonaute protein (Ago2 in humans) where it then interacts with and regulates the mRNA target. (biomedcentral.com)
  • All those approaches exploit the fact that members of orthologous protein families, even if they are strongly diverged, still share a common sequence pattern. (biomedcentral.com)
  • Human mitogen-activated protein kinase activating protein containing death domain (MADD). (embl.de)
  • Others, such as human MADD (MAP (Mitogen-activated protein) kinase activating protein containing death domain) and human ST5 (Suppressor of tumoreginicity 5) gene products are involved in regulation of MAPKs (Mitogen-activated protein kinases) signaling pathways. (embl.de)
  • Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
  • In coding region of DNA, it is imaginable that the nonsynonymous mutations that change the protein sequences would undergo strong selection, and those nonsense mutations that cause pre-mature termination of protein synthesis are also highly deleterious and subjective to purifying selection. (biomedcentral.com)
  • In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. (cshl.edu)
  • At the genic level, single nucleotide polymorphisms (SNPs) in noncoding regions of the human resistin gene were either not significantly associated with insulin resistance ( 4 , 5 ) or associated with an insulin sensitivity index in the case of a different promoter SNP from the one that we present in this article ( 6 ). (diabetesjournals.org)
  • In humans, the orthologous region contains several single nucleotide polymorphisms (SNPs) known to be associated with decreased expression of IFNB1 in activated monocytes, and loops to the IFNB1 gene. (pasteur.fr)
  • Identification of "human accelerated" conserved noncoding sequences (HACNSs). (yale.edu)
  • To this end, we have focused on identifying noncoding sequences highly conserved in nonhuman vertebrate species that display high rates of nucleotide substitution on the human lineage, which may indicate positive selection for new regulatory functions. (yale.edu)
  • To identify putative regulatory sequences evolving rapidly on the human lineage, we developed a test statistic (in collaboration with Shyam Prabhakar of the Genome Institute of Singapore) for assessing the significance of human-specific sequence acceleration in conserved noncoding sequences (CNSs). (yale.edu)
  • Using this approach, we identified 992 conserved noncoding sequences that are evolving rapidly on the human lineage (Fig. 1B and 1C). (yale.edu)
  • We termed these elements human-accelerated conserved noncoding sequences (HACNSs). (yale.edu)
  • We sought to confirm this finding by using an extended set of orthologous sequences. (biomedcentral.com)
  • However, the availability of additional FOXI orthologous sequences from a variety of species, including other primates, has permitted this initial finding to be revised. (biomedcentral.com)
  • Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (embl.de)
  • However, a comprehensive genome-wide map of human S/MARs is yet not available. (researchgate.net)
  • The systematic identification of conserved developmental regulatory elements has made it possible to study the impact of human-specific changes in regulatory DNAs on a genome-wide scale. (yale.edu)
  • Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. (kb.se)
  • These animal models may occur in non-human primates, dogs, cats, goats, mice in which mutations have been induced, or in other less common laboratory species such as bears. (stanford.edu)
  • Different mutations in the human FOXI1 gene and its regulatory binding site on SLC26A4 (also known as pendrin) have been shown to compromise the transcription of this anion transporter gene in patients with Pendred Syndrome and nonsyndromic enlargement of the vestibular aqueduct [ 2 ]. (biomedcentral.com)
  • Overall, these findings have led to the hypothesis that mutations in the human FOXI1 gene might cause sensorineural deafness with distal renal tubular acidosis and male infertility [ 4 ]. (biomedcentral.com)
  • Sequence analysis showed that these "young" Alu insertions represented gene conversion events of pre-existing ancient Alu elements or independent parallel insertions of older Alu elements in the same genomic region. (ojp.gov)
  • We failed to identify any copy number differences within the SHFM3 orthologous genomic locus between Dac mutant and wild-type littermates, showing that the Dactylaplasia alleles are not associated with duplications of the region, in contrast with the described human SHFM3 cases. (unige.ch)
  • The differences between the nature of the human and mouse genomic abnormalities argue against models proposed so far that either envisioned SHFM3 as a local trisomy or Dac as a mutant allele of Fbxw4. (unige.ch)
  • These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions. (biomedcentral.com)
  • These genomic regions appear to have an elevated likelihood of positive selection, based on nucleotide level conservation and transcriptional data. (biomedcentral.com)
  • In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. (biomedcentral.com)
  • The amino acid sequence mediating the bactericidal activity of human BPI (huBPI) is underlined. (elifesciences.org)
  • The study was a large team effort involving researchers in the UK, from the Babraham Institute, the University of Manchester, the Sanger Institute and the University of Cambridge, in Australia, from the University of Melbourne, and the USA, from the University of Texas at San Antonio (all part of the Sequence Analysis of Vertebrate Orthologous Imprinted Regions 'SAVOIR' consortium). (eurekalert.org)
  • Furthermore, other near-human species such as Zeltron, Chiss , and Sullustan share the human ortholog of this locus, which supports the inference that the ancestral sequence was noncoding, and that the GLABR has de novo origins in the Wookiee. (ubc.ca)
  • Anticipated orthologous ORFs in the regions above were defined as BLAT (Kent 2002) or SSearch (Pearson and Lipman 1988) sequence matches. (ubc.ca)
  • Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. (kb.se)
  • HACNSs show a statistically significant excess of human-specific sequence changes (circled) at positions highly conserved in other species. (yale.edu)
  • The second, more practical consideration is that evolutionary conservation provides a means to interpret the statistical and ultimately biological importance of human-specific sequence changes. (yale.edu)
  • In our approach, sites within CNSs were binned based on their degree of sequence conservation in six nonhuman species: chimpanzee, rhesus macaque, mouse, rat, dog and chicken, and human-specific substitutions were identified by parsimony (Fig. 1A). (yale.edu)
  • We are dissecting a number of elements in detail using a synthetic approach, in which subsets of the human-specific sequence changes in each element are transferred into the chimpanzee enhancer sequence. (yale.edu)
  • The human sequence used in this annotation is from the Mar. 2006 (hg18) assembly. (nodai-genome.org)
  • The human sequence used in this annotation is from the Dec. 2013 (GRCh38/hg38) assembly. (noncode.org)
  • Non-hyperlinked coordinates indicate orthologous region in respective other species. (lbl.gov)
  • Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. (embl.de)
  • First, human-specific developmental features, as elaborations on the common theme of mammalian development, are likely to arise in part from changes in the conserved genetic architecture of the developmental regulatory machinery. (yale.edu)
  • We have constructed a second-generation, high-resolution CNV map for the rhesus macaque and combined it with similar CNV data for the chimpanzee and ultra-high-resolution CNV data from humans to determine comprehensively the location and structure of primate CNV hotspots. (biomedcentral.com)
  • In order to identify primate hotspots for CNV formation, we compiled CNV datasets for human, chimpanzee and rhesus macaque. (biomedcentral.com)
  • Research published in Nature Genetics by a team of international scientists including the department of zoology at the University of Melbourne, Australia, has established an identical mechanism of genetic imprinting, a process involved in marsupial and human fetal development, which evolved 150 million years ago. (eurekalert.org)
  • This paper shows that we share a common genetic imprinting mechanism which has been active for about 150 million years despite the differences in reproductive strategies between marsupials and humans," said Professor Geoffrey Shaw of the Department of Zoology at the University of Melbourne, a coauthor on the paper. (eurekalert.org)
  • Because there is no back up copy, when errors occur in this process, it results in many human genetic diseases mainly affecting growth and brain function. (eurekalert.org)
  • Understanding how genetic imprinting evolved is important," said Dr Shaw, "It helps us to determine how the mechanism works and what we can do to avoid the development of a number of human diseases. (eurekalert.org)
  • In addition, the study identified the human genetic variation associated with the L1 insertion polymorphisms in major geographic groups. (ojp.gov)
  • A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer. (pasteur.fr)
  • However, because globally as travelers returned home from affected regions no identical genetic match was found among sequenced ( 6,7 ). (cdc.gov)
  • Concurrent cholera cases in the United States, linked contemporary isolates, a defi nitive genetic origin for the by travel to cholera-endemic regions in Asia and Africa, outbreak in Haiti remains speculative. (cdc.gov)
  • Characterization of a novel human SMC heterodimer homologous to the Schizosaccharomyces pombe Rad18/Spr18 complex. (nih.gov)
  • Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function. (kb.se)
  • My research focused on the identification and characterization of animal models of human diseases. (stanford.edu)
  • One such approach uses linkage studies in rodent models to identify homologous human candidates. (mcw.edu)
  • The LCR encompasses 5 major HSs, each of which is highly homologous among humans, mice, and other mammals. (wustl.edu)
  • Pask explains that the microRNA structure is virtually identical to that of mice and humans, but there was no evidence of this gene or a similar microRNA in the more distantly related platypus. (eurekalert.org)
  • The Dactylaplasia mice display equivalent limb defects and the two corresponding alleles (Dac1j and Dac2j) map in the region syntenic with the duplications in SHFM3. (unige.ch)
  • Functional regions I-III are framed, and positively charged amino acids are shown in blue. (elifesciences.org)
  • B ) Functional regions I-III (dark grey) as shown for huBPI. (elifesciences.org)
  • Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. (researchgate.net)
  • We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. (kb.se)
  • To put worm kinases into an evolutionary and functional context, we compared them with the distant kinomes of human, fly, and yeast. (wormbook.org)
  • These experiments have also provided evidence of functional differences between human and chimpanzee orthologs. (yale.edu)
  • For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. (cshl.edu)
  • Task 3.2-1 Identification of orthologous regions of interest (ROIs) within the rat genome. (euratrans.eu)
  • The location of each human-specific substitution is indicated by a red box above the alignment. (yale.edu)
  • We are using in vivo mouse transgenic assays to examine particular HACNSs from our current dataset for human-specific gene regulatory functions by comparison to chimpanzee and rhesus orthologs (Fig. 3). (yale.edu)
  • Both GIMAP4 and GIMAP7 from human Jurkat cells [ 3 ] localize to the endoplasmic reticulum and Golgi apparatus while mouse Gimap3 from murine IL-3-dependent 32D myeloid precursor cells was expressed at the outer mitochondrial membrane [ 15 ]. (hindawi.com)
  • D ) Number of basic amino acids in regions I-III as shown for oyster BPI (osBPI), scorpionfish BPI (scoBPI), huBPI and murine BPI (muBPI). (elifesciences.org)
  • Here, we show that the deregulation of Ifnb1 expression observed in murine Trim33-/- macrophages correlates with abnormal looping of both ICE and the Ifnb1 gene to a 100 kb downstream region overlapping the Ptplad2/Hacd4 gene. (pasteur.fr)
  • Un-ambiguous orthologs were identified and synteny blocks anchored to these regions. (ubc.ca)
  • The symbol for the orthologous gene in the mouse is Col7a1. (wikipedia.org)
  • Here we report the relative contributions of TE-driven CTCF binding site expansions to conserved and divergent chromatin looping in human and mouse. (nature.com)
  • Animal models offer a unique opportunity to study the pathogenesis of neurologic diseases afflicting both humans and animals. (stanford.edu)
  • Inherited diseases in dogs reliably replicate many hereditary diseases in humans. (stanford.edu)
  • Fungi are ubiquitous airborne allergens and are important causes of human diseases, especially in the upper and lower respiratory tracts. (medscape.com)
  • ous organisms including human. (researchgate.net)
  • 6 families appear to have been lost from nematodes, based on their presence in fly, human and more basal organisms ( Table 1 ), and several new families have been invented within the coelomate lineage, whose functions predominantly map to immunity/angiogenesis, neurobiology, cell cycle and morphogenesis. (wormbook.org)
  • Analysis of the lyp phenotype in the F344 DNA recombinant rats helped us define the critical lyp interval as a region of approximately 33 Kb between D4Rhw6 (76.83 Mb) and IIsnp3 (77.16 Mb) containing Gimap1 , Gimap5 , and Gimap3 (formerly known as Ian2 , Ian5 , and Ian4 , resp. (hindawi.com)
  • Task 3.2-4 Dissemination of priority regions and associated analysis though the ENSEMBL genome browser. (euratrans.eu)
  • This region is a predicted myeloid super-enhancer in which we could characterize 3 myeloid-specific active enhancers, one of which (E5) increases the response of the Ifnb1 promoter to activation. (pasteur.fr)
  • These data were recapitulated in vivo, where G/G homozygotes had significantly higher resistin mRNA levels in human abdominal subcutaneous fat. (diabetesjournals.org)
  • In this report, we demonstrate that deletion of the conserved region of 5'HS 1, 2, 3, 4, or 5/6 abolishes HS formation at the deletion site but has no influence on the formation of the remaining HSs in the LCR. (wustl.edu)
  • Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans, 20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39 worldwide human populations from the HGDP-CEPH diversity panel. (biomedcentral.com)
  • Human-specific substitutions at sites conserved from chimpanzee to chicken are expected to be uncommon events, and were consequently given more weight than substitutions at less conserved sites. (yale.edu)
  • Using three interspecies comparisons, it has been suggested that this may be a gene under human-specific selection. (biomedcentral.com)
  • We present evidence for recent positive selection in the FOXI1 gene region in Africa. (biomedcentral.com)
  • In this study, we identified over 2,000 human CNVs that overlap with orthologous chimpanzee or orthologous macaque CNVs. (biomedcentral.com)
  • In cases where multiple chains align over a particular region of the other genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes. (noncode.org)
  • These loci may have been hotspots of cis-regulatory change throughout human evolution. (yale.edu)
  • Environmentally sensitive hotspots in the methylome of the early human embryo. (who.int)
  • Kinases are deeply conserved in evolution, and the worm has family homologs for over 80% of the human kinome. (wormbook.org)
  • Losses in neuronal density were observed in island and matrix regions during maturation, and differential developmental programmed cell death was observed in islands and matrix regions. (stanford.edu)
  • pendent of those associated with cretory ducts, columnar epithelia the KRAS gene is more frequent- other key mechanistic characteris- lining the gastrointestinal tract and ly mutated in human cancer, which tics of IARC Group 1 carcinogens. (who.int)
  • Prevalence of human papillomavirus types in head and neck cancer sub-sites in the Indian population. (who.int)
  • It can also tolerate gaps in both human and the other genome simultaneously. (noncode.org)