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Col6a3 collagen, type VI, alpha 3 [ Mus musculus (house mouse) ]

Gene ID: 12835, updated on 5-Mar-2024

Summary

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Official Symbol
Col6a3provided by MGI
Official Full Name
collagen, type VI, alpha 3provided by MGI
Primary source
MGI:MGI:88461
See related
Ensembl:ENSMUSG00000048126 AllianceGenome:MGI:88461
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Col6a-3
Summary
Predicted to be an extracellular matrix structural constituent conferring tensile strength. Located in extracellular matrix; extracellular space; and sarcolemma. Part of collagen trimer. Is expressed in several structures, including brain meninges; cardiovascular system; embryo mesenchyme; genitourinary system; and musculoskeletal system. Used to study Ullrich congenital muscular dystrophy and congenital muscular dystrophy. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy; dystonia 27; and muscular dystrophy. Orthologous to human COL6A3 (collagen type VI alpha 3 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in limb E14.5 (RPKM 62.3), subcutaneous fat pad adult (RPKM 60.9) and 17 other tissues See more
Orthologs
human all
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Genomic context

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Location:
1 D; 1 45.53 cM
Exon count:
44
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (90694582..90771710, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (90766860..90844001, complement)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:92591815-92592016 Neighboring gene predicted gene, 35332 Neighboring gene predicted gene, 41918 Neighboring gene STARR-seq mESC enhancer starr_01688 Neighboring gene STARR-seq mESC enhancer starr_01689 Neighboring gene predicted gene, 35381 Neighboring gene melanophilin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The impact of endotrophin on the progression of chronic liver disease. Kim M, et al. Exp Mol Med, 2020 Oct. PMID 33110211, Free PMC Article
  2. COL6A3-derived endotrophin links reciprocal interactions among hepatic cells in the pathology of chronic liver disease. Lee C, et al. J Pathol, 2019 Jan. PMID 30246318
  3. COL6A3 protein deficiency in mice leads to muscle and tendon defects similar to human collagen VI congenital muscular dystrophy. Pan TC, et al. J Biol Chem, 2013 May 17. PMID 23564457, Free PMC Article
  4. Alternative splicing of transcripts for the alpha 3 chain of mouse collagen VI: identification of an abundant isoform lacking domains N7-N10 in mouse and human. Dziadek M, et al. Matrix Biol, 2002 Apr. PMID 12009329
  5. Type VI collagen and its cleavage product, endotrophin, cooperatively regulate the adipogenic and lipolytic capacity of adipocytes. Oh J, et al. Metabolism, 2021 Jan. PMID 33188786

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The impact of endotrophin on the progression of chronic liver disease.
    Title: The impact of endotrophin on the progression of chronic liver disease.
  2. In temporomandibular joint osteoarthritis, membrane-bound NG2 is found to colocalize with pericellular type VI collagen in superficial layer cells in the mandibular condylar cartilage perichondrium but is present at high levels in the cytosol of chondroblastic and hypertrophic cells.
    Title: Neuron/Glial Antigen 2-Type VI Collagen Interactions During Murine Temporomandibular Joint Osteoarthritis.
  3. COL6A3-derived endotrophin is a crucial mediator in reciprocal interactions among various hepatic cell populations in the pathogenesis of chronic liver disease.
    Title: COL6A3-derived endotrophin links reciprocal interactions among hepatic cells in the pathology of chronic liver disease.
  4. Overexpression of endotrophin caused upregulation of adipogenic genes in the white adipose tissue(WAT) of endotrophin transgenic mice. The mice exhibited inhibited lipolysis and accelerated hypertrophy and hyperplasia in WAT.
    Title: Divergent functions of endotrophin on different cell populations in adipose tissue.
  5. Data indicate that overexpression of endotrophin (COL6alpha3) locally in adipose tissue promotes metabolic dysfunction under a high-fat diet (HFD) challenge.
    Title: Endotrophin triggers adipose tissue fibrosis and metabolic dysfunction.
  6. Data show that the TFIID subunit TAF4 is essential to restrain the growth promoting properties of collagen 6A3 (Col6a3).
    Title: TAF4 inactivation reveals the 3 dimensional growth promoting activities of collagen 6A3.
  7. mice lacking normal alpha3(VI) collagen chains display mild musculoskeletal phenotypes similar to mice deficient in the alpha1(VI) collagen alpha chain, suggesting that alpha3(VI) collagen does not elicit essential functions in normal growth and development
    Title: COL6A3 protein deficiency in mice leads to muscle and tendon defects similar to human collagen VI congenital muscular dystrophy.
  8. analysis of collagen VI chains alpha4, alpha5, and alpha6with high homology to the alpha3 chain
    Title: Three novel collagen VI chains with high homology to the alpha3 chain.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (7) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within neuron apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen trimer IDA
Inferred from Direct Assay
more info
 PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular matrix ISO
Inferred from Sequence Orthology
more info
 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in sarcolemma IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
collagen alpha-3(VI) chain
Names
collagen alpha 3 chain type VI
collagen alpha3(VI)
procollagen, type VI, alpha 3
type VI collagen alpha 3 subunit

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.

mRNA and Protein(s)

  1. NM_001243008.1 → NP_001229937.1  collagen alpha-3(VI) chain isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA118378, AC110895, AC158773, AF034136, AK076391, BQ560536, BQ561449, BX638221, CF734596, CJ098732, CN667533, FQ976558
    UniProtKB/TrEMBL
    E9PWQ3
    Related
    ENSMUSP00000057131.10, ENSMUST00000056925.16
    Conserved Domains (7) summary
    pfam01391
    Location:2305 → 2362
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1836 → 1991
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:1432 → 1596
    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:3227 → 3278
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:3109 → 3177
    fn3; Fibronectin type III domain
    pfam00092
    Location:1636 → 1807
    VWA; von Willebrand factor type A domain
    cl00057
    Location:443 → 607
    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_001243009.1 → NP_001229938.1  collagen alpha-3(VI) chain isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks 3 non-consecutive in-frame coding exons compared to variant 1. This results in a shorter isoform (2) missing two internal protein segments compared to isoform 1.
    Source sequence(s)
    AA118378, AC110895, AC158773, AK076391, BQ560536, BQ561449, BX638221, CF734596, CJ098732, FQ976558
    Consensus CDS
    CCDS56640.1
    UniProtKB/TrEMBL
    A0A087WS16, J3QQ16
    Related
    ENSMUSP00000137585.2, ENSMUST00000097653.11
    Conserved Domains (7) summary
    pfam01391
    Location:1698 → 1755
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1229 → 1384
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:825 → 989
    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:2620 → 2671
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:2502 → 2570
    fn3; Fibronectin type III domain
    pfam00092
    Location:1029 → 1200
    VWA; von Willebrand factor type A domain
    cl00057
    Location:36 → 200
    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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    90694582..90771710 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030245436.2 → XP_030101296.1  collagen alpha-3(VI) chain isoform X1

    UniProtKB/TrEMBL
    E9PWQ3
    Conserved Domains (7) summary
    pfam01391
    Location:2105 → 2162
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1636 → 1791
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:1232 → 1396
    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:3027 → 3078
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:2909 → 2977
    fn3; Fibronectin type III domain
    pfam00092
    Location:1436 → 1607
    VWA; von Willebrand factor type A domain
    cl00057
    Location:443 → 607
    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_030245437.2 → XP_030101297.1  collagen alpha-3(VI) chain isoform X2

    UniProtKB/TrEMBL
    E9PWQ3
    Conserved Domains (7) summary
    pfam01391
    Location:2096 → 2154
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1630 → 1785
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:1226 → 1390
    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:3021 → 3072
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:2903 → 2971
    fn3; Fibronectin type III domain
    pfam00092
    Location:1430 → 1601
    VWA; von Willebrand factor type A domain
    cl00057
    Location:237 → 401
    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_030245438.2 → XP_030101298.1  collagen alpha-3(VI) chain isoform X3

    UniProtKB/TrEMBL
    A0A087WS16
    Conserved Domains (7) summary
    pfam01391
    Location:1895 → 1953
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1429 → 1584
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:1025 → 1189
    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:2820 → 2871
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:2702 → 2770
    fn3; Fibronectin type III domain
    pfam00092
    Location:1229 → 1400
    VWA; von Willebrand factor type A domain
    cl00057
    Location:36 → 200
    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_030245451.2 → XP_030101311.1  collagen alpha-3(VI) chain isoform X4

    UniProtKB/TrEMBL
    A0A087WS16
    Conserved Domains (7) summary
    pfam01391
    Location:1503 → 1560
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:1034 → 1189
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:630 → 794
    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:2425 → 2476
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:2307 → 2375
    fn3; Fibronectin type III domain
    pfam00092
    Location:834 → 1005
    VWA; von Willebrand factor type A domain
    cl00057
    Location:427 → 589
    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 ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_009935.1: Suppressed sequence

    Description
    NM_009935.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
Nucleotide Protein Strain
Heading Accession and Version

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