Col6a4 collagen, type VI, alpha 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col6a4provided by RGD
Official Full Name: collagen, type VI, alpha 4provided by RGD
Primary source: RGD:1564060
See related: EnsemblRapid:ENSRNOG00000031782 AllianceGenome:RGD:1564060
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
Also known as: Dvwa; Col6a4p1; RGD1564060
Summary: Predicted to enable collagen binding activity. Predicted to be involved in extracellular matrix organization. Predicted to be located in extracellular matrix and extracellular region. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward (RPKM 358.5) See more
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Genomic context

Location:: 8q32

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (115495886..115612229, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (106617169..106733493, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (114670628..114766803, complement)

Chromosome 8 - NC_086026.1 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: 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

AU024783 (e-PCR)
- UniSTS:179970

D8Got207 (e-PCR)
- UniSTS:115418

D11S3831 (e-PCR)
- UniSTS:153061

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables collagen binding	IEA Inferred from Electronic Annotation more info

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

Component	Evidence Code	Pubs
located_in extracellular matrix	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-4(VI) chain

Names: collagen, type VI, alpha 4 pseudogene 1; 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_001412226.1 → NP_001399155.1 collagen alpha-4(VI) chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/TrEMBL

F1M6H4

Related

ENSRNOP00000042470.5, ENSRNOT00000047563.6

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

115495886..115612229 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039081569.2 → XP_038937497.1 collagen alpha-4(VI) chain isoform X1

UniProtKB/TrEMBL

A0A8I6A6Y7, F1M6H4

Related

ENSRNOP00000086989.1, ENSRNOT00000111160.2

Conserved Domains (5) summary

cd01450
Location:1806 → 1988

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:672 → 828

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:854 → 1023

VWA; von Willebrand factor type A domain

pfam01391
Location:1512 → 1567

Collagen; Collagen triple helix repeat (20 copies)

cl00057
Location:233 → 384

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_001271182.1: Suppressed sequence

Description

NM_001271182.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.