Col5a3 collagen type V alpha 3 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col5a3provided by RGD
Official Full Name: collagen type V alpha 3 chainprovided by RGD
Primary source: RGD:70922
See related: Ensembl:ENSRNOG00000020525 AllianceGenome:RGD:70922
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables proteoglycan binding activity. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell-matrix adhesion. Located in collagen-containing extracellular matrix. Orthologous to human COL5A3 (collagen type V alpha 3 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 132.2), Heart (RPKM 94.0) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q13

Exon count:: 69

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (27580768..27626002, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (19304564..19349809, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (21786324..21831751, 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?

Alpha4(V) collagen has an important role in peripheral nerve terminal differentiation. alpha4(V) collagen coassembles with laminin on the surface of polarized Schwann cells to form tube-like ECM structures that are sites of myelination.
Title: Glypican-1 and alpha4(V) collagen are required for Schwann cell myelination.
N-terminal globular domain of the pro-alpha3(V) chain influence bone formation of osteoblasts through proteoglycan on the cell surface during development or regeneration
Title: Pro-alpha3(V) collagen chain is expressed in bone and its basic N-terminal peptide adheres to osteosarcoma cells.
alpha4(V)-NTD binding occurs via a mechanism that requires the high affinity heparin binding site and that is blocked by soluble heparin.
Title: Constitutive release of alpha4 type V collagen N-terminal domain by Schwann cells and binding to cell surface and extracellular matrix heparan sulfate proteoglycans.

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General gene information

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Markers

D8Rat53 (e-PCR), detects polymorphism
- UniSTS:119120

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	ISO Inferred from Sequence Orthology more info
enables proteoglycan binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of collagen type V trimer	ISO Inferred from Sequence Orthology more info
part_of collagen type V trimer	TAS Traceable Author Statement more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay 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-3(V) chain

Names: collagen, type V, alpha 3; collagen, type V, alpha 4; procollagen, type V, 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_021760.1 → NP_068528.1 collagen alpha-3(V) chain precursor

See identical proteins and their annotated locations for NP_068528.1

Status: PROVISIONAL

Source sequence(s)

AF272661

UniProtKB/TrEMBL

Q9JI04

Conserved Domains (3) summary

pfam01391
Location:722 → 780

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1508 → 1735

COLFI; Fibrillar collagen C-terminal domain

cl22861
Location:32 → 211

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

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

27580768..27626002 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039082051.2 → XP_038937979.1 collagen alpha-3(V) chain isoform X1

UniProtKB/TrEMBL

F7EVZ0

Related

ENSRNOP00000027897.4

Conserved Domains (4) summary

PHA03169
Location:643 → 823

PHA03169; hypothetical protein; Provisional

pfam01391
Location:724 → 779

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1506 → 1734

COLFI; Fibrillar collagen C-terminal domain

cl22861
Location:31 → 210

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_039082052.2 → XP_038937980.1 collagen alpha-3(V) chain isoform X2

Conserved Domains (3) summary

PHA03169
Location:333 → 513

PHA03169; hypothetical protein; Provisional

pfam01391
Location:414 → 469

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1196 → 1424

COLFI; Fibrillar collagen C-terminal domain
XM_063266064.1 → XP_063122134.1 collagen alpha-3(V) chain isoform X3
XM_039082054.2 → XP_038937982.1 collagen alpha-3(V) chain isoform X5

Conserved Domains (2) summary

pfam01391
Location:39 → 94

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:821 → 1049

COLFI; Fibrillar collagen C-terminal domain
XM_039082053.2 → XP_038937981.1 collagen alpha-3(V) chain isoform X4

Conserved Domains (2) summary

pfam01391
Location:64 → 119

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:846 → 1074

COLFI; Fibrillar collagen C-terminal domain