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

    Gene ID: 1293, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:2213
    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; UCMD1C; BTHLM1C
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL6A3 in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (237324018..237414164, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (237815093..237905193, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (238232661..238322807, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:238126819-238127349 Neighboring gene uncharacterized LOC105373954 Neighboring gene VISTA enhancer hs1951 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:238233151-238234350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238242415-238242916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238244426-238244926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238244927-238245427 Neighboring gene Sharpr-MPRA regulatory region 1020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238275487-238275986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238341552-238342058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238354812-238355347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238356546-238357046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238357047-238357547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238359577-238360252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238360253-238360930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17366 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:238368147-238369346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12478 Neighboring gene uncharacterized LOC105373957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238394761-238395729 Neighboring gene Sharpr-MPRA regulatory region 758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238406043-238406543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238419044-238419544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:238419545-238420045 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

    Clone Names

    • FLJ34702, FLJ98399, DKFZp686N0262, DKFZp686D23123, DKFZp686K04147

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables serine-type endopeptidase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle organ development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to UV IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to glucose 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)

    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_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
      A8MT30, B4E3U5, B7ZMJ7, E9PFQ6, E9PGQ9, P12111, Q16501, Q53QF4, Q53QF6
      UniProtKB/TrEMBL
      D9ZGF2
      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/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/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/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_057167.4NP_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/TrEMBL
      B7ZW00
      Related
      ENSP00000315873.4, ENST00000353578.9
      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: 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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      237324018..237414164 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      237815093..237905193 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)