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

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: human all
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Genomic context

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_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The impact of endotrophin on the progression of chronic liver disease.
Title: The impact of endotrophin on the progression of chronic liver disease.
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.
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.
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.
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.
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.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation
Endonuclease-mediated (6)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI507288 (e-PCR)
- UniSTS:178436

AI042932 (e-PCR)
- UniSTS:178439

01.MMHAP90FLA1.seq (e-PCR)
- UniSTS:122678

AF064749 (e-PCR)
- UniSTS:158827

Homology

Homologs of the Col6a3 gene: The Col6a3 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 332 organisms have orthologs with human gene Col6a3
Orthologs

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

Component	Evidence Code	Pubs
part_of collagen trimer	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info	PubMed
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)

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

Q9Z0I9

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 ...
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

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: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

90694582..90771710 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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 ...
XM_030245437.2 → XP_030101297.1 collagen alpha-3(VI) chain isoform X2

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 ...
XM_030245438.2 → XP_030101298.1 collagen alpha-3(VI) chain isoform X3

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 ...
XM_030245451.2 → XP_030101311.1 collagen alpha-3(VI) chain isoform X4

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

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.