Col4a6 collagen, type IV, alpha 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col4a6provided by MGI
Official Full Name: collagen, type IV, alpha 6provided by MGI
Primary source: MGI:MGI:2152695
See related: Ensembl:ENSMUSG00000031273 AllianceGenome:MGI:2152695
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
Summary: An extracellular matrix structural constituent. Acts upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and extracellular matrix organization. Located in basement membrane. Part of collagen type IV trimer. Is expressed in several structures, including bone; meninges; oral region epithelium; sensory organ; and trunk. Human ortholog(s) of this gene implicated in AMME complex and X-linked deafness 6. Orthologous to human COL4A6 (collagen type IV alpha 6 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in bladder adult (RPKM 12.0), ovary adult (RPKM 3.7) and 15 other tissues See more
Orthologs: human all
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Genomic context

Location:: X F1- F2; X 61.8 cM

Exon count:: 46

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (139948399..140257091, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (141165403..141474095, complement)

Chromosome X - NC_000086.8 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?

Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice.
Title: Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice.
These findings indicate that alpha112:alpha556 (IV) network, which is the only network that includes the alpha6(IV) chain, is one regulator of KRT10 expression in keratinization of oral mucosal epithelium.
Title: Type IV collagen α6 chain is a regulator of keratin 10 in keratinization of oral mucosal epithelium.
although alpha5 and alpha6 (IV) chains are induced in the glomerular basement membrane in autosomal recessive Alport syndrome, their induction does not seem to play a major compensatory role
Title: COL4A6 is dispensable for autosomal recessive Alport syndrome.
In murine embryos, collagen IV subunits alpha1(IV), alpha2(IV), alpha5(IV) and alpha6(IV) were detected in the basement membrane surrounding the lens vesicle, and they persisted in the capsule until adulthood.
Title: Collagen IV in the developing lens capsule.
the proximal bifunctional promoter regulates the expression of the alpha5(IV) and alpha6(IV) genes in a cell-specific manner and demonstrates promoter plasticity in growth factor regulation of type IV collagen genes in different tissues of the body.
Title: Bifunctional promoter of type IV collagen COL4A5 and COL4A6 genes regulates the expression of alpha5 and alpha6 chains in a distinct cell-specific fashion.

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Variation

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Alleles

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

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

General gene information

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Markers

DXMit67 (e-PCR), detects polymorphism
- UniSTS:116513

px-16e7 (e-PCR)
- UniSTS:257329

BB116301 (e-PCR)
- UniSTS:186186

px-5d2 (e-PCR)
- UniSTS:258001

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IDA Inferred from Direct Assay more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
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 cellular response to amino acid stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in collagen-activated tyrosine kinase receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within extracellular matrix organization	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IV trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-6(IV) chain

Names: procollagen, type IV, alpha 6

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_053185.3 → NP_444415.2 collagen alpha-6(IV) chain precursor

Status: VALIDATED

Source sequence(s)

AL691493, AL713983

Consensus CDS

CCDS41153.1

UniProtKB/TrEMBL

B1AVK5, Q9ESQ1

Related

ENSMUSP00000098765.3, ENSMUST00000101205.3

Conserved Domains (2) summary

pfam01391
Location:1401 → 1460

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1576 → 1688

C4; C-terminal tandem repeated domain in type 4 procollagen

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_000086.8 Reference GRCm39 C57BL/6J

Range

139948399..140257091 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011247883.4 → XP_011246185.1 collagen alpha-6(IV) chain isoform X1

UniProtKB/TrEMBL

Q9ESQ1

Conserved Domains (3) summary

pfam01391
Location:1377 → 1436

Collagen; Collagen triple helix repeat (20 copies)

pfam09606
Location:1080 → 1439

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam01413
Location:1552 → 1664

C4; C-terminal tandem repeated domain in type 4 procollagen