Col6a4 collagen, type VI, alpha 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col6a4provided by MGI
Official Full Name: collagen, type VI, alpha 4provided by MGI
Primary source: MGI:MGI:1915803
See related: Ensembl:ENSMUSG00000032572 AllianceGenome:MGI:1915803
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: Dvwa; Vwa6; EG235580; 1110001D15Rik
Summary: Enables collagen binding activity. Involved in extracellular matrix organization. Located in extracellular region. Part of protein-containing complex. Is active in extracellular matrix. Is expressed in several structures, including bone; genitourinary system; gut; musculature; and spleen. Orthologous to human COL6A4P1 (collagen type VI alpha 4 pseudogene 1) and COL6A4P2 (collagen type VI alpha 4 pseudogene 2). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in subcutaneous fat pad adult (RPKM 42.4), ovary adult (RPKM 23.3) and 5 other tissues See more
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Genomic context

Location:: 9 F1; 9 57.39 cM

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (105867284..105975729, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (105990318..106096828, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data 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 collagen VI alpha 4 chain is strongly expressed in the intestinal smooth muscle, surrounding the follicles in ovary, and in testis
Title: Differential and restricted expression of novel collagen VI chains in mouse.
DVWA is evolutionally very unique, which, together with its specific expression in articular cartilage, suggests its specific role in human cartilage metabolism.
Title: Cloning and characterization of the osteoarthritis-associated gene DVWA.
discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix
Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).
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)

Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU024783 (e-PCR)
- UniSTS:179970

AU023415 (e-PCR)
- UniSTS:179971

AI413310 (e-PCR)
- UniSTS:165663

PMC186647P1 (e-PCR)
- UniSTS:271716

Col6a4 (e-PCR), detects polymorphism
- UniSTS:536469

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables collagen binding	IPI Inferred from Physical Interaction more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: collagen alpha-4(VI) chain

Names: double von Willebrand factor A domains; dual von Willebrand factor A domains

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_026763.3 → NP_081039.2 collagen alpha-4(VI) chain precursor

See identical proteins and their annotated locations for NP_081039.2

Status: VALIDATED

Source sequence(s)

AC120386

Consensus CDS

CCDS52907.1

UniProtKB/Swiss-Prot

A2AX52, A2AX53, A2AX54, A9CR35

Related

ENSMUSP00000112472.2, ENSMUST00000121963.3

Conserved Domains (6) summary

PHA03169
Location:1400 → 1663

PHA03169; hypothetical protein; Provisional

cd01450
Location:1981 → 2163

vWFA_subfamily_ECM; 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 ...

cd01472
Location:234 → 399

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam00092
Location:1030 → 1198

VWA; von Willebrand factor type A domain

pfam01391
Location:1595 → 1654

Collagen; Collagen triple helix repeat (20 copies)

cl00057
Location:429 → 580

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

NC_000075.7 Reference GRCm39 C57BL/6J

Range

105867284..105975729 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036155227.1 → XP_036011120.1 collagen alpha-4(VI) chain isoform X1

UniProtKB/Swiss-Prot

A2AX52, A2AX53, A2AX54, A9CR35

Conserved Domains (6) summary

PHA03169
Location:1400 → 1663

PHA03169; hypothetical protein; Provisional

cd01450
Location:1981 → 2163

vWFA_subfamily_ECM; 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 ...

cd01472
Location:234 → 399

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam00092
Location:1030 → 1198

VWA; von Willebrand factor type A domain

pfam01391
Location:1595 → 1654

Collagen; Collagen triple helix repeat (20 copies)

cl00057
Location:429 → 580

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_030244544.2 → XP_030100404.1 collagen alpha-4(VI) chain isoform X2

Conserved Domains (4) summary

pfam01391
Location:1592 → 1654

Collagen; Collagen triple helix repeat (20 copies)

cd01472
Location:234 → 399

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam00092
Location:1030 → 1198

VWA; von Willebrand factor type A domain

cl00057
Location:429 → 580

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_011242907.3 → XP_011241209.1 collagen alpha-4(VI) chain isoform X3

Conserved Domains (3) summary

cd01472
Location:234 → 399

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam00092
Location:1030 → 1198

VWA; von Willebrand factor type A domain

cl00057
Location:34 → 196

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 ...