Col4a5 collagen type IV alpha 5 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Col4a5provided by RGD
Official Full Name: collagen type IV alpha 5 chainprovided by RGD
Primary source: RGD:1565499
See related: EnsemblRapid:ENSRNOG00000018951 AllianceGenome:RGD:1565499
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: RGD1565499
Summary: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within collagen-activated tyrosine kinase receptor signaling pathway and neuromuscular junction development. Predicted to be located in neuromuscular junction. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Used to study proteinuria. Human ortholog(s) of this gene implicated in Alport syndrome and X-linked Alport syndrome. Orthologous to human COL4A5 (collagen type IV alpha 5 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 378.4), Heart (RPKM 277.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq33

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (109907251..110111214)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (105118762..105322699)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (112769595..112983720)

Chromosome X - NC_086039.1 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 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?

Creation of X-linked Alport syndrome rat model with Col4a5 deficiency.
Title: Creation of X-linked Alport syndrome rat model with Col4a5 deficiency.
Glomerular collagen alpha5(IV) chains protein was higher and more intense in immunofluorescence staining according to diabetic durations.
Title: Regulation of type IV collagen alpha chains of glomerular epithelial cells in diabetic conditions.

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General gene information

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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

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available 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 neuromuscular junction development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen type IV trimer	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: collagen alpha-5(IV) chain

Names: collagen, type IV, alpha 5; procollagen, type IV, alpha 5

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_001426996.1 → NP_001413925.1 collagen alpha-5(IV) chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A0A8I5ZZ86

Related

ENSRNOP00000104853.1, ENSRNOT00000142543.1

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_086039.1 Reference GRCr8

Range

109907251..110111214

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006257313.3 → XP_006257375.1 collagen alpha-5(IV) chain isoform X1

See identical proteins and their annotated locations for XP_006257375.1

Related

ENSRNOP00000085447.2, ENSRNOT00000108925.2

Conserved Domains (2) summary

pfam01391
Location:1074 → 1132

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1573 → 1682

C4; C-terminal tandem repeated domain in type 4 procollagen
XM_063280126.1 → XP_063136196.1 collagen alpha-5(IV) chain isoform X2