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COL6A2 collagen type VI alpha 2 chain [ Homo sapiens (human) ]

Gene ID: 1292, updated on 21-Dec-2017
Official Symbol
COL6A2provided by HGNC
Official Full Name
collagen type VI alpha 2 chainprovided by HGNC
Primary source
HGNC:HGNC:2212
See related
Ensembl:ENSG00000142173 MIM:120240; Vega:OTTHUMG00000090489
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
UCMD1; BTHLM1; PP3610
Summary
This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in placenta (RPKM 164.0), endometrium (RPKM 155.3) and 22 other tissues See more
Orthologs
Location:
21q22.3
Exon count:
30
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 21 NC_000021.9 (46098071..46132849)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47518033..47552763)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene vegetative cell wall protein gp1 Neighboring gene proteasome subunit alpha 6 pseudogene 3 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene spermatogenesis and centriole associated 1 like

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • 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 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...
  • 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...
  • 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ46862, DKFZp586E1322

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
collagen catabolic process TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
protein heterotrimerization IPI
Inferred from Physical Interaction
more info
PubMed 
response to glucose IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular matrix HDA PubMed 
extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with 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
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
extracellular vesicle HDA PubMed 
protein complex IPI
Inferred from Physical Interaction
more info
PubMed 
proteinaceous extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
sarcolemma IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-2(VI) chain
Names
collagen VI, alpha-2 polypeptide
collagen, type VI, alpha 2
human mRNA for collagen VI alpha-2 C-terminal globular domain

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_008675.1 RefSeqGene

    Range
    5001..39731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_476

mRNA and Protein(s)

  1. NM_001849.3NP_001840.3  collagen alpha-2(VI) chain isoform 2C2 precursor

    See identical proteins and their annotated locations for NP_001840.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2C2), that differs from the other variants in the last exon, encodes the full-length protein.
    Source sequence(s)
    AL044156, AY029208, BC065509, CN352095, CN352155
    Consensus CDS
    CCDS13728.1
    UniProtKB/Swiss-Prot
    P12110
    Related
    ENSP00000300527.4, OTTHUMP00000115568, ENST00000300527.8, OTTHUMT00000206971
    Conserved Domains (3) summary
    pfam01391
    Location:439498
    Collagen; Collagen triple helix repeat (20 copies)
    cd01480
    Location:612803
    vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
    pfam00092
    Location:8331007
    VWA; von Willebrand factor type A domain
  2. NM_058174.2NP_478054.2  collagen alpha-2(VI) chain isoform 2C2a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2C2a) has a different last exon than the other variants. Isoform 2C2a is 101 amino acids shorter than isoform 2C2 and 91 amino acids longer than isoform 2C2a'.
    Source sequence(s)
    AI275476, BC065509, BM989656, CN352095, CN352155, X15977
    Consensus CDS
    CCDS13729.1
    UniProtKB/Swiss-Prot
    P12110
    Related
    ENSP00000380870.1, OTTHUMP00000115569, ENST00000397763.5, OTTHUMT00000206972
    Conserved Domains (2) summary
    pfam01391
    Location:439498
    Collagen; Collagen triple helix repeat (20 copies)
    cd01480
    Location:612803
    vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
  3. NM_058175.2NP_478055.2  collagen alpha-2(VI) chain isoform 2C2a' precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2C2a') encodes the shortest polypeptide. The last exon in this variant results in the use of a stop codon that shortens the protein by 192 amino acids compared to the full-length protein, although the transcripts are nearly the same length.
    Source sequence(s)
    AI275476, BC065509, BM989656, CN352095, CN352155, M34570
    Consensus CDS
    CCDS13730.1
    UniProtKB/Swiss-Prot
    P12110
    Related
    ENSP00000312529.5, ENST00000310645.9
    Conserved Domains (2) summary
    pfam01391
    Location:439498
    Collagen; Collagen triple helix repeat (20 copies)
    cd01480
    Location:612803
    vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p7 Primary Assembly

    Range
    46098071..46132849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529451.1XP_011527753.1  collagen alpha-2(VI) chain isoform X1

    See identical proteins and their annotated locations for XP_011527753.1

    UniProtKB/Swiss-Prot
    P12110
    Conserved Domains (3) summary
    pfam01391
    Location:439498
    Collagen; Collagen triple helix repeat (20 copies)
    cd01480
    Location:612803
    vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
    pfam00092
    Location:8331007
    VWA; von Willebrand factor type A domain

RNA

  1. XR_937438.2 RNA Sequence

  2. XR_937439.2 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018932.2 Alternate CHM1_1.1

    Range
    47078809..47113491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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