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    COL6A5 collagen type VI alpha 5 chain [ Homo sapiens (human) ]

    Gene ID: 256076, updated on 3-Dec-2024

    Summary

    Official Symbol
    COL6A5provided by HGNC
    Official Full Name
    collagen type VI alpha 5 chainprovided by HGNC
    Primary source
    HGNC:HGNC:26674
    See related
    Ensembl:ENSG00000172752 MIM:611916; AllianceGenome:HGNC:26674
    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
    VWA4; COL29A1
    Summary
    This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
    Expression
    Biased expression in skin (RPKM 1.9), lung (RPKM 1.6) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL6A5 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (130345672..130484846)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (133089679..133228818)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (130064515..130203690)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374106 Neighboring gene ATP5MC2 pseudogene 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:130126750-130127949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:130161092-130161649 Neighboring gene MPRA-validated peak4833 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14733 Neighboring gene collagen type VI alpha 6 chain Neighboring gene ReSE screen-validated silencer GRCh37_chr3:130297667-130297916 Neighboring gene phosphoinositide-3-kinase regulatory subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20523

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-02)

    ClinGen Genome Curation Page
    Haploinsufficency

    Dosage sensitivity unlikely (Last evaluated 2021-02-02)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General protein information

    Preferred Names
    collagen alpha-5(VI) chain
    Names
    collagen, type VI, alpha 5
    collagen, type XXIX, alpha 1
    von Willebrand factor A domain-containing protein 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_021424.2 RefSeqGene

      Range
      5002..144176
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001278298.2NP_001265227.1  collagen alpha-5(VI) chain isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the allele encoded by the GRCh38 reference genome and encodes isoform (1).
      Source sequence(s)
      AC093004, AC117398, KF573676
      Consensus CDS
      CCDS93384.1
      UniProtKB/Swiss-Prot
      A8TX70, A9J6L2, A9J6L4, A9J6L6, A9J6L7, A9J6M0, A9J6M1, A9J6M2, B5MEA7, Q6ZW26, Q8NA36
      UniProtKB/TrEMBL
      H0Y393
      Related
      ENSP00000362250.5, ENST00000373157.9
      Conserved Domains (6) summary
      pfam01391
      Location:15641623
      Collagen; Collagen triple helix repeat (20 copies)
      COG2304
      Location:445593
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:22902467
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cd01472
      Location:627787
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam00092
      Location:814985
      VWA; von Willebrand factor type A domain
      cl00057
      Location:29195
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    2. NM_001412157.1NP_001399086.1  collagen alpha-5(VI) chain isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses the same exon combination as variant 1 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. The encoded isoform (3) has a frameshifted C-terminus compared to isoform 1.
      Source sequence(s)
      CP068275
      UniProtKB/Swiss-Prot
      A8TX70, A9J6L2, A9J6L4, A9J6L6, A9J6L7, A9J6M0, A9J6M1, A9J6M2, B5MEA7, Q6ZW26, Q8NA36
    3. NM_153264.7NP_694996.5  collagen alpha-5(VI) chain isoform 2 precursor

      Status: REVIEWED

      Source sequence(s)
      AC093004, AC117398, KF573676
      Consensus CDS
      CCDS93385.1
      UniProtKB/Swiss-Prot
      A8TX70, A9J6L2, A9J6L4, A9J6L6, A9J6L7, A9J6M0, A9J6M1, A9J6M2, B5MEA7, Q6ZW26, Q8NA36
      Related
      ENSP00000422898.2, ENST00000512836.6
      Conserved Domains (6) summary
      cd01450
      Location:22902467
      vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cd01472
      Location:627787
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam01391
      Location:13941447
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00092
      Location:814985
      VWA; von Willebrand factor type A domain
      NF038329
      Location:14781730
      gly_rich_SclB; LPXTG-anchored collagen-like adhesin Scl2/SclB
      cl00057
      Location:29195
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    RNA

    1. NR_022012.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC093004, AC117398, KF573676
      Related
      ENST00000312481.11

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      130345672..130484846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      133089679..133228818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)