Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 256076, updated on 13-Feb-2019

    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
    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

    Genomic context

    See COL6A5 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (130345516..130484846)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (130064359..130203690)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374106 Neighboring gene ATP synthase membrane subunit c locus 2 pseudogene Neighboring gene collagen type VI alpha 6 chain Neighboring gene phosphoinositide-3-kinase regulatory subunit 4

    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

    NHGRI GWAS Catalog

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

    Pathways from BioSystems

    • 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...
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • 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...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • 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 KEGG)
      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...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved 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...
    • NCAM signaling for neurite out-growth, organism-specific biosystem (from REACTOME)
      NCAM signaling for neurite out-growth, organism-specific biosystemThe neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the n...
    • NCAM1 interactions, organism-specific biosystem (from REACTOME)
      NCAM1 interactions, organism-specific biosystemThe neural cell adhesion molecule, NCAM1 is generally considered as a cell adhesion mediator, but it is also considered to be a signal transducing receptor molecule. NCAM1 is involved in multiple cis...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • 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...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Signaling by PDGF, organism-specific biosystem (from REACTOME)
      Signaling by PDGF, organism-specific biosystemPlatelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary end...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Homology

    Clone Names

    • FLJ35880

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent conferring tensile strength IEA
    Inferred from Electronic Annotation
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    collagen-containing extracellular matrix HDA PubMed 
    colocalizes_with collagen-containing extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    extracellular region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     

    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)

    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_021424.1 RefSeqGene

      Range
      5001..144332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI743837, AM906083, EU085556
      UniProtKB/Swiss-Prot
      A8TX70
      Related
      ENSP00000265379.7, ENST00000265379.10
      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_153264.6NP_694996.5  collagen alpha-5(VI) chain isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI743837, AK123718, EU085556
      UniProtKB/Swiss-Prot
      A8TX70
      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 ...

    RNA

    1. NR_022012.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI743837, EU085556
      Related
      ENST00000312481.11

    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_000003.12 Reference GRCh38.p12 Primary Assembly

      Range
      130345516..130484846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512621.2XP_011510923.1  collagen alpha-5(VI) chain isoform X1

      Conserved Domains (6) summary
      pfam01391
      Location:15791636
      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:22692446
      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. XM_011512623.2XP_011510925.1  collagen alpha-5(VI) chain isoform X3

      Conserved Domains (5) 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]
      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 ...
    3. XM_011512622.2XP_011510924.1  collagen alpha-5(VI) chain isoform X2

      Conserved Domains (5) 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]
      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 ...
    Support Center