Col5a1 collagen type V alpha 1 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col5a1provided by RGD
Official Full Name: collagen type V alpha 1 chainprovided by RGD
Primary source: RGD:70920
See related: Ensembl:ENSRNOG00000008749 AllianceGenome:RGD:70920
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 heparin binding activity. Predicted to be involved in several processes, including collagen biosynthetic process; collagen fibril organization; and wound healing, spreading of epidermal cells. Predicted to act upstream of or within several processes, including circulatory system development; skin development; and tendon development. Predicted to be located in basement membrane. Predicted to be part of collagen type V trimer. Predicted to be active in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and Ehlers-Danlos syndrome classic type 1. Orthologous to human COL5A1 (collagen type V alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Uterus (RPKM 349.4), Muscle (RPKM 271.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3p12

Exon count:: 68

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (31606475..31755097)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (11208429..11356715)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (6430180..6581010)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Results describe the effect of collagen Va1/2 on the fibrillogenesis of Sprague-Dawley rat tenocytes, as well as the efficacy of Col V siRNA engineered tenocytes for tendon tissue engineering.
Title: Col V siRNA engineered tenocytes for tendon tissue engineering.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH139630 (e-PCR)
- UniSTS:221714

Col5a1 (e-PCR), detects polymorphism
- UniSTS:531584

RH128099 (e-PCR)
- UniSTS:211407

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
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables heparin binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	ISO Inferred from Sequence Orthology more info
enables platelet-derived growth factor binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info
enables proteoglycan binding	IEA Inferred from Electronic Annotation more info
enables proteoglycan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in blood vessel development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blood vessel development	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in cell migration	ISO Inferred from Sequence Orthology more info
involved_in collagen biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in collagen biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in collagen fibril organization	ISO Inferred from Sequence Orthology more info
involved_in eye morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in eye morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in heart morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within heart morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in integrin biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in integrin biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endodermal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cellular component organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cellular component organization	ISO Inferred from Sequence Orthology more info
involved_in skin development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skin development	ISO Inferred from Sequence Orthology more info
involved_in skin development	ISO Inferred from Sequence Orthology more info
involved_in supramolecular fiber organization	ISO Inferred from Sequence Orthology more info
involved_in tendon development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within tendon development	ISO Inferred from Sequence Orthology more info
involved_in wound healing, spreading of epidermal cells	IEA Inferred from Electronic Annotation more info
involved_in wound healing, spreading of epidermal cells	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen trimer	ISO Inferred from Sequence Orthology more info
part_of collagen type V trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type V trimer	IEA Inferred from Electronic Annotation more info
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	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

General protein information

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Preferred Names: collagen alpha-1(V) chain

Names: collagen alpha 1 (V); collagen, type V, alpha 1; procollagen, type V, alpha 1

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_134452.2 → NP_604447.2 collagen alpha-1(V) chain precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

Q9JI03

UniProtKB/TrEMBL

A6JTM0

Related

ENSRNOP00000084311.1, ENSRNOT00000110258.1

Conserved Domains (3) summary

smart00210
Location:41 → 230

TSPN; Thrombospondin N-terminal -like domains

pfam01391
Location:876 → 932

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1609 → 1838

COLFI; Fibrillar collagen C-terminal domain

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_086021.1 Reference GRCr8

Range

31606475..31755097

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233873.5 → XP_006233935.1 collagen alpha-1(V) chain isoform X1

UniProtKB/Swiss-Prot

Q9JI03

UniProtKB/TrEMBL

G3V763

Related

ENSRNOP00000012334.8

Conserved Domains (3) summary

pfam01391
Location:873 → 932

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:41 → 230

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1612 → 1838

COLFI; Fibrillar collagen C-terminal domain
XM_063284748.1 → XP_063140818.1 collagen alpha-1(V) chain isoform X2