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

Gene ID: 12835, updated on 8-Dec-2022

Summary

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
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Genomic context

See Col6a3 in Genome Data Viewer
Location:
1 D; 1 45.53 cM
Exon count:
44
Annotation release Status Assembly Chr Location
109 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 predicted gene, 35332 Neighboring gene predicted gene, 41918 Neighboring gene predicted gene, 35381 Neighboring gene melanophilin

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (6) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

General protein information

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_001243008.1NP_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
    Q9Z0I9
    Related
    ENSMUSP00000057131.10, ENSMUST00000056925.16
    Conserved Domains (7) summary
    pfam01391
    Location:23052362
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:18361991
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:14321596
    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:32273278
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:31093177
    fn3; Fibronectin type III domain
    pfam00092
    Location:16361807
    VWA; von Willebrand factor type A domain
    cl00057
    Location:443607
    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_001243009.1NP_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
    J3QQ16
    Related
    ENSMUSP00000137585.2, ENSMUST00000097653.11
    Conserved Domains (7) summary
    pfam01391
    Location:16981755
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:12291384
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:825989
    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:26202671
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:25022570
    fn3; Fibronectin type III domain
    pfam00092
    Location:10291200
    VWA; von Willebrand factor type A domain
    cl00057
    Location:36200
    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: Mus musculus 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 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_030245436.2XP_030101296.1  collagen alpha-3(VI) chain isoform X1

    Conserved Domains (7) summary
    pfam01391
    Location:21052162
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:16361791
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:12321396
    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:30273078
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:29092977
    fn3; Fibronectin type III domain
    pfam00092
    Location:14361607
    VWA; von Willebrand factor type A domain
    cl00057
    Location:443607
    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_030245437.2XP_030101297.1  collagen alpha-3(VI) chain isoform X2

    Conserved Domains (7) summary
    pfam01391
    Location:20962154
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:16301785
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:12261390
    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:30213072
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:29032971
    fn3; Fibronectin type III domain
    pfam00092
    Location:14301601
    VWA; von Willebrand factor type A domain
    cl00057
    Location:237401
    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_030245438.2XP_030101298.1  collagen alpha-3(VI) chain isoform X3

    Conserved Domains (7) summary
    pfam01391
    Location:18951953
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:14291584
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:10251189
    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:28202871
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:27022770
    fn3; Fibronectin type III domain
    pfam00092
    Location:12291400
    VWA; von Willebrand factor type A domain
    cl00057
    Location:36200
    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_030245451.2XP_030101311.1  collagen alpha-3(VI) chain isoform X4

    Conserved Domains (7) summary
    pfam01391
    Location:15031560
    Collagen; Collagen triple helix repeat (20 copies)
    smart00327
    Location:10341189
    VWA; von Willebrand factor (vWF) type A domain
    cd01481
    Location:630794
    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:24252476
    Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
    pfam00041
    Location:23072375
    fn3; Fibronectin type III domain
    pfam00092
    Location:8341005
    VWA; von Willebrand factor type A domain
    cl00057
    Location:427589
    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.