Col4a3 collagen type IV alpha 3 chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Col4a3provided by RGD
Full Name: collagen type IV alpha 3 chainprovided by RGD
Primary source: RGD:71085
See related: EnsemblRapid:ENSRNOG00000015365 AllianceGenome:RGD:71085
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 integrin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in response to glucose. Predicted to be located in endoplasmic reticulum. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Used to study glomerulonephritis. Human ortholog(s) of this gene implicated in Alport syndrome; autosomal dominant Alport syndrome; autosomal recessive Alport syndrome; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A3 (collagen type IV alpha 3 chain). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Kidney (RPKM 688.0), Lung (RPKM 331.8) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q34

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (91323990..91453088)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (83875849..84004955)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (88357528..88484735)

Chromosome 9 - NC_086027.1 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 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?

COL4A mutations comprise a frequent cause of Familial microscopic hematuria.
Title: Frequent COL4 mutations in familial microhematuria accompanied by later-onset Alport nephropathy due to focal segmental glomerulosclerosis.
These findings suggested that artesunate attenuates alveolitis and pulmonary fibrosis by regulating expression of collagen-IV, TIMP-1 and 2, as well as MMP-2 and -9, to reduce ECM accumulation.
Title: Artesunate modulates expression of matrix metalloproteinases and their inhibitors as well as collagen-IV to attenuate pulmonary fibrosis in rats.
Data show that collagen type III (Col3), collagen type IV (Col4) and p38 mitogen-activated protein kinase (p38 MAPK) are up-regulated in models of diabetic nephropathy.
Title: [Down-regulation of p38 MAPK and collagen by 1, 25-(OH)2-VD3 in rat models of diabetic nephropathy].
Glomerular collagen alpha3(IV) 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.
Segregation of experimental autoimmune glomerulonephritis as a complex genetic trait and exclusion of Col4a3 as a candidate gene. No significant linkage was detected in the region of rat chromosome 9 where Col4a3 is localized.
Title: Segregation of experimental autoimmune glomerulonephritis as a complex genetic trait and exclusion of Col4a3 as a candidate gene.
only few residues in the nephritogenic T-cell epitope pCol(28-40) were critical; pCol(28-40) is a potential nephritogenic T-cell epitope in Goodpasture's syndrome.
Title: Characterization of the T-cell epitope that causes anti-GBM glomerulonephritis.
Downregulation of alpha3(IV) and enhancement of the matrix metalloproteinase-2 activity in the glomeruli may contribute to the glomerular damage by altering the glomerular basement membrane components.
Title: Altered expression of matrix-related molecules in the development of chronic Thy1.1 nephritis.
The T cell epitope pCol(28-40) of noncollagen domain 1 of collagen type IV alpha 3 chain not only uniformly induces severe glomerulonephritis but also elicits anti-GBM antibodies in 76% of immunized rats after prominent glomerular injury in a rat model.
Title: A self T cell epitope induces autoantibody response: mechanism for production of antibodies to diverse glomerular basement membrane antigens.
results suggest the activated MMP-9 induced by TNFalpha cleaves the existing collagen network in the extracellular matrix, perturbing the Sertoli cell TJ-barrier; this creates a negative feedback causing TNFalpha to induce collagen alpha3(IV) and TIMP-1
Title: The interplay of collagen IV, tumor necrosis factor-alpha, gelatinase B (matrix metalloprotease-9), and tissue inhibitor of metalloproteases-1 in the basal lamina regulates Sertoli cell-tight junction dynamics in the rat testis.

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General gene information

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Markers

D9Wox12 (e-PCR)
- UniSTS:518926

BE110813 (e-PCR)
- UniSTS:245319

OMM1056 (e-PCR)
- UniSTS:512138

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 integrin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in activation of cysteine-type endopeptidase activity involved in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in activation of cysteine-type endopeptidase activity involved in apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in glomerular basement membrane development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vascular endothelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to glucose	IEP Inferred from Expression Pattern more info	PubMed

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
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-3(IV) chain

Names: collagen alpha-3(IV) chain-like; collagen, type IV, alpha 3 (Goodpasture antigen); procollagen, type IV, 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_001413988.1 → NP_001400917.1 collagen alpha-3(IV) chain precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

F1LRJ1

Related

ENSRNOP00000108770.1, ENSRNOT00000111608.2

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

91323990..91453088

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083897.2 → XP_038939825.1 collagen alpha-3(IV) chain isoform X1

Conserved Domains (2) summary

pfam01391
Location:657 → 711

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:940 → 1050

C4; C-terminal tandem repeated domain in type 4 procollagen