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    COL5A1 collagen type V alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1289, updated on 21-Apr-2019

    Summary

    Official Symbol
    COL5A1provided by HGNC
    Official Full Name
    collagen type V alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2209
    See related
    Ensembl:ENSG00000130635 MIM:120215
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EDSC; EDSCL1
    Summary
    This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
    Expression
    Broad expression in placenta (RPKM 45.0), endometrium (RPKM 38.1) and 16 other tissues See more
    Orthologs

    Genomic context

    See COL5A1 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    68
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (134641789..134844843)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137533651..137736689)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376311 Neighboring gene uncharacterized LOC100506532 Neighboring gene COL5A1 antisense RNA 1 Neighboring gene uncharacterized LOC101448202 Neighboring gene microRNA 3689c Neighboring gene microRNA 3689a

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Ehlers-Danlos syndrome, classic type
    MedGen: C4552122 OMIM: 130000 GeneReviews: Classic Ehlers-Danlos Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2017-12-14)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2017-12-14)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    A genome-wide association study of central corneal thickness in Latinos.
    NHGRI GWA Catalog
    Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.
    NHGRI GWA Catalog
    Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
    NHGRI GWA Catalog
    Joint influence of small-effect genetic variants on human longevity.
    NHGRI GWA Catalog
    Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease.
    NHGRI GWA Catalog
    New loci associated with central cornea thickness include COL5A1, AKAP13 and AVGR8.
    NHGRI GWA Catalog
    Population-based meta-analysis in Caucasians confirms association with COL5A1 and ZNF469 but not COL8A2 with central corneal thickness.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of collagen, type V, alpha 1 (COL5A1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Allograft Rejection, organism-specific biosystem (from WikiPathways)
      Allograft Rejection, organism-specific biosystemThis pathway illustrates molecular interactions involved in the fundamental adaptive immune response for allograft destruction. This pathway was adapted in large part from the KEGG pathway http://www...
    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
      miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ45760

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent conferring tensile strength HDA PubMed 
    extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integrin binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    platelet-derived growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    proteoglycan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    eye morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    integrin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of endodermal cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of cellular component organization IEA
    Inferred from Electronic Annotation
    more info
     
    skin development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    supramolecular fiber organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tendon development IEA
    Inferred from Electronic Annotation
    more info
     
    wound healing, spreading of epidermal cells IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    collagen alpha-1(V) chain
    Names
    collagen, type V, alpha 1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008030.1 RefSeqGene

      Range
      5000..208038
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_737

    mRNA and Protein(s)

    1. NM_000093.4NP_000084.3  collagen alpha-1(V) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_000084.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399221, CN399265, CN484933, ES314363
      Consensus CDS
      CCDS6982.1
      UniProtKB/Swiss-Prot
      P20908
      UniProtKB/TrEMBL
      A0A024R8E5, B2ZZ86, Q59EE7
      Related
      ENSP00000360882.3, ENST00000371817.7
      Conserved Domains (3) summary
      pfam01391
      Location:871930
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:39230
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:16101836
      COLFI; Fibrillar collagen C-terminal domain
    2. NM_001278074.1NP_001265003.1  collagen alpha-1(V) chain isoform 2 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2 which is of the same length but contains an alternate segment, compared to isoform 1. This variant is based on experimental data in PMID 22149965 and is supported by partial transcripts and RNA-seq data.
      Source sequence(s)
      AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399198, CN399221, CN399265, CN484933, ES314363
      Consensus CDS
      CCDS75932.1
      UniProtKB/TrEMBL
      A0A087WXW9, B2ZZ86, Q59EE7
      Related
      ENSP00000481360.1, ENST00000618395.4
      Conserved Domains (3) summary
      pfam01391
      Location:871930
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:39230
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:16101836
      COLFI; Fibrillar collagen C-terminal domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

      Range
      134641789..134844843
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017014266.2XP_016869755.1  collagen alpha-1(V) chain isoform X1

    RNA

    1. XR_001746183.1 RNA Sequence

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