Col4a6 collagen type IV alpha 6 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col4a6provided by RGD
Official Full Name: collagen type IV alpha 6 chainprovided by RGD
Primary source: RGD:1589724
See related: EnsemblRapid:ENSRNOG00000056772 AllianceGenome:RGD:1589724
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to be an extracellular matrix structural constituent. Predicted to act upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and extracellular matrix organization. Predicted to be located in basement membrane. Predicted to be part of collagen type IV trimer. Human ortholog(s) of this gene implicated in X-linked deafness 6. Orthologous to human COL4A6 (collagen type IV alpha 6 chain). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 65.0), Uterus (RPKM 36.4) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq33

Exon count:: 46

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (109554945..109905987, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (104766463..105117499, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (112405647..112768337, complement)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

AU047046 (e-PCR)
- UniSTS:110895

AU049795 (e-PCR)
- UniSTS:146241

RH132646 (e-PCR)
- UniSTS:215929

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen type IV trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	ISO Inferred from Sequence Orthology more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
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: collagen, 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.