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

Gene ID: 1292, updated on 25-Jan-2024

Summary

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; AllianceGenome:HGNC:2212
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
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Genomic context

See COL6A2 in Genome Data Viewer
Location:
21q22.3
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46098112..46132848)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44476193..44510935)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47518026..47552762)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene proteasome subunit alpha 6 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47500021-47500530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47504842-47505342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47505343-47505843 Neighboring gene COL6A2 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12001 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:47527125-47527884 Neighboring gene uncharacterized LOC124905043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47551971-47552475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47556247-47557020 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47560109-47560298 Neighboring gene Sharpr-MPRA regulatory region 3768 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47571745-47572448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47572449-47573154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573155-47573858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573859-47574562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47574563-47575266 Neighboring gene FTCD antisense RNA 1 Neighboring gene spermatogenesis and centriole associated 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590104-47590604 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590605-47591105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47600015-47600618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47602435-47603038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47603039-47603642

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

  • FLJ46862, DKFZp586E1322

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
 
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-2(VI) chain
Names
collagen VI, alpha-2 polypeptide
collagen, type VI, alpha 2
epididymis secretory sperm binding protein
human mRNA for collagen VI alpha-2 C-terminal globular domain

NCBI Reference Sequences (RefSeq)

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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_001849.4NP_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)
    AP001471, AY029208, BC065509, CN352095, CN352155
    Consensus CDS
    CCDS13728.1
    UniProtKB/Swiss-Prot
    P12110, Q13909, Q13910, Q13911, Q14048, Q14049, Q16259, Q16597, Q6P0Q1, Q9UML3, Q9Y4S8
    UniProtKB/TrEMBL
    A0A384MDP3
    Related
    ENSP00000300527.4, ENST00000300527.9
    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_058174.3NP_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, AP001471, BC065509, BM989656, CN352095, CN352155, X15977
    Consensus CDS
    CCDS13729.1
    UniProtKB/Swiss-Prot
    P12110
    Related
    ENSP00000380870.1, ENST00000397763.6
    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_058175.3NP_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, AP001471, BC065509, BM989656, CN352095, CN352155, M34570
    Consensus CDS
    CCDS13730.1
    UniProtKB/Swiss-Prot
    P12110
    Related
    ENSP00000387115.1, ENST00000409416.6
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    46098112..46132848
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    44476193..44510935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)