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COL6A3 collagen type VI alpha 3 chain [ Homo sapiens (human) ]

Gene ID: 1293, updated on 3-Jun-2018
Official Symbol
COL6A3provided by HGNC
Official Full Name
collagen type VI alpha 3 chainprovided by HGNC
Primary source
HGNC:HGNC:2213
See related
Ensembl:ENSG00000163359 MIM:120250; Vega:OTTHUMG00000150020
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
DYT27; UCMD1; BTHLM1
Summary
This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. 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 the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]
Expression
Broad expression in gall bladder (RPKM 140.2), endometrium (RPKM 95.0) and 16 other tissues See more
Orthologs
See COL6A3 in Genome Data Viewer
Location:
2q37.3
Exon count:
50
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (237324012..237434822, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238232655..238322850, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373954 Neighboring gene VISTA enhancer hs1951 Neighboring gene uncharacterized LOC105373957 Neighboring gene melanophilin Neighboring gene microRNA 6811

  • 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 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

  • FLJ34702, FLJ98399, DKFZp686N0262, DKFZp686D23123, DKFZp686K04147

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
growth plate cartilage chondrocyte morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
muscle organ development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-3(VI) chain
Names
collagen VI, alpha-3 polypeptide
collagen, type VI, alpha 3

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_008676.1 RefSeqGene

    Range
    5001..95196
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_473

mRNA and Protein(s)

  1. NM_004369.3NP_004360.2  collagen alpha-3(VI) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_004360.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the full-length isoform (1).
    Source sequence(s)
    AK092021, AK308451, BC033174, BU687672, BX647500, DC411101, X52022
    Consensus CDS
    CCDS33412.1
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    D9ZGF2, Q63HQ4, Q8N4Z1
    Related
    ENSP00000295550.4, OTTHUMP00000195994, ENST00000295550.8, OTTHUMT00000315790
    Conserved Domains (7) summary
    pfam01391
    Location:23142371
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:29933061
    FN3; Fibronectin type 3 domain
    smart00327
    Location:18381994
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:14351599
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:31113162
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:16391811
    VWA; von Willebrand factor type A domain
    cl00057
    Location:10281191
    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_057164.4NP_476505.3  collagen alpha-3(VI) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_476505.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK092021, BX647500, DC411101
    Consensus CDS
    CCDS54439.1
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    Q63HQ4
    Related
    ENSP00000375860.2, OTTHUMP00000195996, ENST00000392003.6, OTTHUMT00000315792
    Conserved Domains (2) summary
    cd01481
    Location:37201
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    cl00057
    Location:621784
    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. NM_057165.4NP_476506.3  collagen alpha-3(VI) chain isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK304870, BX647500, DC411101
    Consensus CDS
    CCDS33411.2
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    Q63HQ4
    Related
    ENSP00000375861.3, OTTHUMP00000195995, ENST00000392004.7, OTTHUMT00000315791
    Conserved Domains (2) summary
    cd01481
    Location:238402
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    cl00057
    Location:822985
    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 ...
  4. NM_057166.4NP_476507.3  collagen alpha-3(VI) chain isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks three alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    BC144595, BC171790, BU687672, DC411101
    Consensus CDS
    CCDS33410.2
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    B7ZW00
    Related
    ENSP00000418285.1, OTTHUMP00000213923, ENST00000472056.5, OTTHUMT00000353032
    Conserved Domains (7) summary
    pfam01391
    Location:17071764
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:23862454
    FN3; Fibronectin type 3 domain
    smart00327
    Location:12311387
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:828992
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:25042555
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:10321204
    VWA; von Willebrand factor type A domain
    cl00057
    Location:421584
    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 ...
  5. NM_057167.3NP_476508.2  collagen alpha-3(VI) chain isoform 5 precursor

    See identical proteins and their annotated locations for NP_476508.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.
    Source sequence(s)
    AK092021, AK308451, BC033174, BU687672, BX647500, DC411101, X52022
    Consensus CDS
    CCDS33409.1
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    Q63HQ4, Q8N4Z1
    Related
    ENSP00000315873.4, ENST00000353578.8
    Conserved Domains (7) summary
    pfam01391
    Location:21082165
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:27872855
    FN3; Fibronectin type 3 domain
    smart00327
    Location:16321788
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:12291393
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:29052956
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:14331605
    VWA; von Willebrand factor type A domain
    cl00057
    Location:822985
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    237324012..237434822 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003304.1XP_016858793.1  collagen alpha-3(VI) chain isoform X5

    Conserved Domains (7) summary
    pfam01391
    Location:15121569
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:21912259
    FN3; Fibronectin type 3 domain
    smart00327
    Location:10361192
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:633797
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:23092360
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:8371009
    VWA; von Willebrand factor type A domain
    cl00057
    Location:226389
    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_005246065.1XP_005246122.1  collagen alpha-3(VI) chain isoform X3

    See identical proteins and their annotated locations for XP_005246122.1

    Conserved Domains (7) summary
    pfam01391
    Location:21142171
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:27932861
    FN3; Fibronectin type 3 domain
    smart00327
    Location:16381794
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:12351399
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:29112962
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:14391611
    VWA; von Willebrand factor type A domain
    cl00057
    Location:828991
    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_006712253.1XP_006712316.1  collagen alpha-3(VI) chain isoform X2

    See identical proteins and their annotated locations for XP_006712316.1

    Conserved Domains (7) summary
    pfam01391
    Location:21472204
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:28262894
    FN3; Fibronectin type 3 domain
    smart00327
    Location:16711827
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:444608
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:29442995
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:14721644
    VWA; von Willebrand factor type A domain
    cl00057
    Location:10281191
    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 ...
  4. XM_011510574.1XP_011508876.1  collagen alpha-3(VI) chain isoform X1

    Conserved Domains (7) summary
    pfam01391
    Location:23132370
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:29923060
    FN3; Fibronectin type 3 domain
    smart00327
    Location:18371993
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:14341598
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:31103161
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:16381810
    VWA; von Willebrand factor type A domain
    cl00057
    Location:10281191
    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 ...
  5. XM_024452684.1XP_024308452.1  collagen alpha-3(VI) chain isoform X4

    Conserved Domains (7) summary
    pfam01391
    Location:19071964
    Collagen; Collagen triple helix repeat (20 copies)
    smart00060
    Location:25862654
    FN3; Fibronectin type 3 domain
    smart00327
    Location:14311587
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:10281192
    vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...
    pfam00014
    Location:27042755
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00092
    Location:12321404
    VWA; von Willebrand factor type A domain
    cl00057
    Location:621784
    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 ...
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