Col4a3 collagen, type IV, alpha 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col4a3provided by MGI
Official Full Name: collagen, type IV, alpha 3provided by MGI
Primary source: MGI:MGI:104688
See related: Ensembl:ENSMUSG00000079465 AllianceGenome:MGI:104688
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: [a]3(IV); alpha3(IV)
Summary: Predicted to enable integrin binding activity. Predicted to be an extracellular matrix structural constituent. Involved in cell surface receptor signaling pathway; glomerular basement membrane development; and negative regulation of angiogenesis. Acts upstream of or within collagen-activated tyrosine kinase receptor signaling pathway. Located in basement membrane. Part of collagen type IV trimer. Is expressed in several structures, including cardiovascular system; eye; foregut; genitourinary system; and trachea. Used to study autosomal recessive Alport syndrome. 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, Apr 2022]
Expression: Biased expression in kidney adult (RPKM 16.1), lung adult (RPKM 12.8) and 2 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1 C5; 1 42.32 cM

Exon count:: 53

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (82564647..82699778)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (82586921..82722059)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Col4a3(-/-) mice present a model of heart failure with preserved ejection fraction secondary to chronic kidney disease wherein OPN and OGDHL are intermediates.
Title: Osteopontin Promotes Left Ventricular Diastolic Dysfunction Through a Mitochondrial Pathway.
The quality and quantity of alpha3IV-NC1-specific Ab and T cell responses are critical for the phenotype of the glomerulonephritis.
Title: Glomerulopathy induced by immunization with a peptide derived from the goodpasture antigen α3IV-NC1.
Report novel mouse model of Alport syndrome with accumulation abnormal collagen alpha3alpha4alpha5(IV) trimers in the glomerular basement membrane.
Title: A mouse Col4a4 mutation causing Alport glomerulosclerosis with abnormal collagen α3α4α5(IV) trimers.
Report monoclonal antibody against the collagen type IV alpha3NC1 domain as a marker for glomerular disease.
Title: A human monoclonal antibody against the collagen type IV α3NC1 domain is a non-invasive optical biomarker for glomerular diseases.
Data show that deletion of tumstatin and TSP1 in p53-/- mice leads to increased tumor burden and reduced survival.
Title: Counterbalancing angiogenic regulatory factors control the rate of cancer progression and survival in a stage-specific manner.
the pathogenetic role of USAG-1 in Col4a3-/- mice might involve crosstalk between kidney tubules and the glomerulus and that inhibition of USAG-1 may be a promising therapeutic approach for the treatment of Alport syndrome.
Title: Loss of the BMP antagonist USAG-1 ameliorates disease in a mouse model of the progressive hereditary kidney disease Alport syndrome.
Collagen alpha 3 alpha 4 alpha 5(IV) originates solely from podocytes; therefore, glomerular Alport disease is a genetic defect that manifests specifically within this cell type.
Title: Cellular origins of type IV collagen networks in developing glomeruli.
Upregulation of Lama5 transcription and concentration of laminin alpha1 and alpha5 within (Alport)collagen alpha3(IV) knockout glomerular basement membrane thickenings contribute to abnormal permeabilities.
Title: Laminin compensation in collagen alpha3(IV) knockout (Alport) glomeruli contributes to permeability defects.
CCR1-mediated recruitment and local activation of macrophages contribute to disease progression in COL4A3-deficient mice. CCR1 is potential therapeutic target for Alport disease or other progressive nephropathies with interstitial macrophage infiltrates.
Title: Delayed chemokine receptor 1 blockade prolongs survival in collagen 4A3-deficient mice with Alport disease.
Collagen alpha3(IV) nor alpha4(IV) were detected in the lens capsule 2 weeks postnatal.
Title: Collagen IV in the developing lens capsule.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (7) 1 citation
Endonuclease-mediated (5) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D1Mit44 (e-PCR), detects polymorphism
- UniSTS:128808

D1Mit254 (e-PCR), detects polymorphism
- UniSTS:128599

Col4a3 (e-PCR), detects polymorphism
- UniSTS:479152

D1Mit382 (e-PCR), detects polymorphism
- UniSTS:128743

AI314140 (e-PCR)
- UniSTS:178420

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
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

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
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 type IV trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IV trimer	ISO Inferred from Sequence Orthology more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation 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

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-3(IV) chain

Names: collagen type IV alpha3 chain; procollagen, type IV, alpha 3; tumstatin

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_007734.3 → NP_031760.2 collagen alpha-3(IV) chain precursor

See identical proteins and their annotated locations for NP_031760.2

Status: VALIDATED

Source sequence(s)

AC123746, AC138214

Consensus CDS

CCDS35631.1

UniProtKB/Swiss-Prot

Q61430, Q61435, Q8CCD6, Q9QZS0

Related

ENSMUSP00000109084.3, ENSMUST00000113457.9

Conserved Domains (2) summary

pfam01391
Location:1377 → 1436

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1445 → 1551

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

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

82564647..82699778

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157135.1 → XP_036013028.1 collagen alpha-3(IV) chain isoform X1

Conserved Domains (1) summary

pfam01391
Location:286 → 339

Collagen; Collagen triple helix repeat (20 copies)