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

Gene ID: 1293, updated on 13-Aug-2020

Summary

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
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

Genomic context

See COL6A3 in Genome Data Viewer
Location:
2q37.3
Exon count:
50
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34702, FLJ98399, DKFZp686N0262, DKFZp686D23123, DKFZp686K04147

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 
serine-type endopeptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
muscle organ development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
collagen alpha-3(VI) chain
Names
collagen VI, alpha-3 polypeptide
collagen, type VI, alpha 3
epididymis secretory sperm binding protein

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_008676.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_004369.4NP_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, X52022
    Consensus CDS
    CCDS33412.1
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    D9ZGF2, Q63HQ4, Q8N4Z1
    Related
    ENSP00000295550.4, ENST00000295550.9
    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_057164.5NP_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, ENST00000392003.6
    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_057165.5NP_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
    Consensus CDS
    CCDS33411.2
    UniProtKB/Swiss-Prot
    P12111
    UniProtKB/TrEMBL
    Q63HQ4
    Related
    ENSP00000375861.3, ENST00000392004.7
    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_057166.5NP_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, ENST00000472056.5
    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
    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 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 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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