Col6a3 collagen type VI alpha 3 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col6a3provided by RGD
Official Full Name: collagen type VI alpha 3 chainprovided by RGD
Primary source: RGD:1308704
See related: EnsemblRapid:ENSRNOG00000019648 AllianceGenome:RGD:1308704
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 enable serine-type endopeptidase inhibitor activity. Involved in response to glucose. Predicted to be located in extracellular matrix and sarcolemma. Predicted to be part of collagen trimer. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); chronic kidney disease; dystonia 27; muscular dystrophy (multiple); and primary open angle glaucoma. Orthologous to human COL6A3 (collagen type VI alpha 3 chain). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Uterus (RPKM 934.7), Lung (RPKM 607.4) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q36

Exon count:: 44

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (98809171..98887060, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (91361578..91439434, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (97926784..98004643, complement)

Chromosome 9 - NC_086027.1 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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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Got112 (e-PCR)
- UniSTS:114472

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

D9Mco92 (e-PCR)
- UniSTS:526170

RH129385 (e-PCR)
- UniSTS:212692

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables serine-type endopeptidase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to UV	ISO Inferred from Sequence Orthology more info
involved_in response to glucose	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	ISO Inferred from Sequence Orthology more info
located_in extracellular matrix	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: collagen alpha-3(VI) chain

Names: collagen, type VI, alpha 3; procollagen, type VI, alpha 3

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_001427497.1 → NP_001414426.1 collagen alpha-3(VI) chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A8I5ZTR6, A0A8I6AHL9

Related

ENSRNOP00000093441.1, ENSRNOT00000026719.7

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_086027.1 Reference GRCr8

Range

98809171..98887060 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063267519.1 → XP_063123589.1 collagen alpha-3(VI) chain isoform X1

UniProtKB/TrEMBL

A6JQM5
XM_063267520.1 → XP_063123590.1 collagen alpha-3(VI) chain isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001109008.1: Suppressed sequence

Description

NM_001109008.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from chicken: COL6A3 (GeneID:396548).