Col4a1 collagen, type IV, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col4a1provided by MGI
Official Full Name: collagen, type IV, alpha 1provided by MGI
Primary source: MGI:MGI:88454
See related: Ensembl:ENSMUSG00000031502 AllianceGenome:MGI:88454
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Bru; Raw; Svc; Col4a-1
Summary: This gene encodes the alpha-1 subunit of the type IV collagens, an essential component of basement membranes. The encoded protein forms a triple helical heterotrimer comprised of two alpha-1 and one alpha-2 subunits that assembles into a type IV collagen network. This gene is located adjacent to the gene encoding alpha-2 subunit. Mice lacking both the alpha-1 and alpha-2 subunits of collagen IV die in utero due to structural deficiencies in the basement membranes and certain mutations in this gene cause perinatal cerebral hemorrhage and porencephaly. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2015]
Expression: Broad expression in subcutaneous fat pad adult (RPKM 160.4), lung adult (RPKM 107.4) and 21 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 8 A1.1; 8 5.53 cM

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (11248423..11362889, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (11198423..11312889, complement)

Chromosome 8 - NC_000074.7 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?

Collagen IV deficiency causes hypertrophic remodeling and endothelium-dependent hyperpolarization in small vessel disease with intracerebral hemorrhage.
Title: Collagen IV deficiency causes hypertrophic remodeling and endothelium-dependent hyperpolarization in small vessel disease with intracerebral hemorrhage.
TGFbeta Signaling Dysregulation May Contribute to COL4A1-Related Glaucomatous Optic Nerve Damage.
Title: TGFβ Signaling Dysregulation May Contribute to COL4A1-Related Glaucomatous Optic Nerve Damage.
A temporally-restricted pattern of endothelial cell collagen 4 alpha 1 expression during embryonic development determined with a novel knockin Col4a1-P2A-eGFP mouse line.
Title: A temporally-restricted pattern of endothelial cell collagen 4 alpha 1 expression during embryonic development determined with a novel knockin Col4a1-P2A-eGFP mouse line.
Impaired intracellular Ca[2+] signaling contributes to age-related cerebral small vessel disease in Col4a1 mutant mice.
Title: Impaired intracellular Ca(2+) signaling contributes to age-related cerebral small vessel disease in Col4a1 mutant mice.
Elevated TGFbeta signaling contributes to cerebral small vessel disease in mouse models of Gould syndrome.
Title: Elevated TGFβ signaling contributes to cerebral small vessel disease in mouse models of Gould syndrome.
Elevated TGFbeta signaling contributes to ocular anterior segment dysgenesis in Col4a1 mutant mice.
Title: Elevated TGFβ signaling contributes to ocular anterior segment dysgenesis in Col4a1 mutant mice.
Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome.
Title: Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome.
COL4A1 Mutations are associated with Neuromuscular Disease.
Title: COL4A1 Mutations Cause Neuromuscular Disease with Tissue-Specific Mechanistic Heterogeneity.
Smooth muscle cell degeneration is a critical factor underlying the partial penetrance of COL4A1-stroke related macrohaemorrhages.
Title: Severity of arterial defects in the retina correlates with the burden of intracerebral haemorrhage in COL4A1-related stroke.
This work presents binding data consistent with a major role of 3-hydroxyproline in interactions of collagen IV with glycoprotein VI and nidogens 1 and 2.
Title: Post-translational modification of type IV collagen with 3-hydroxyproline affects its interactions with glycoprotein VI and nidogens 1 and 2.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

Go to the top of the page Help

Associated conditions

Description	Tests
bruised GeneReviews: Not available
retinal anteriolar wiring GeneReviews: Not available
small with vacuolar cataract GeneReviews: Not available

Variation

Go to the top of the page Help

Alleles

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

Chemically induced (ENU) (9) 1 citation
Chemically induced (other) (2) 1 citation
Endonuclease-mediated (4)
Radiation induced (2) 1 citation
Targeted (3) 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

Col4a1 (e-PCR), detects polymorphism
- UniSTS:472864

Col4a1 (e-PCR), detects polymorphism
- UniSTS:141370

Col4a1 (e-PCR), detects polymorphism
- UniSTS:496710

Col4a1 (e-PCR), detects polymorphism
- UniSTS:545920

D0Nds29 (e-PCR), detects polymorphism
- UniSTS:141461

RH128563 (e-PCR)
- UniSTS:211871

J04694 (e-PCR)
- UniSTS:179696

Gene Ontology Provided by MGI

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 extracellular matrix structural constituent conferring tensile strength	ISO Inferred from Sequence Orthology more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables platelet-derived growth factor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in basement membrane organization	IEA Inferred from Electronic Annotation more info
involved_in basement membrane organization	ISO Inferred from Sequence Orthology more info
involved_in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in branching involved in blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to amino acid stimulus	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 epithelial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuromuscular junction development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in renal tubule morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in renal tubule morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in retinal blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in retinal blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
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
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(IV) chain

Names: alpha-1 type IV collagen; alpha1(IV) collagen; procollagen, type IV, alpha 1

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_009931.2 → NP_034061.2 collagen alpha-1(IV) chain precursor

See identical proteins and their annotated locations for NP_034061.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.

Source sequence(s)

AC114598, AC115800, AK147661, CJ108618, CJ248638

Consensus CDS

CCDS40219.1

UniProtKB/Swiss-Prot

P02463, Q3UHJ4, Q3UJE7, Q3UQV2, Q53X35, Q6GQS7, Q6PHB5, Q99LQ8

UniProtKB/TrEMBL

A0A1B0GSI7

Related

ENSMUSP00000033898.10, ENSMUST00000033898.10

Conserved Domains (2) summary

pfam01391
Location:1088 → 1147

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1556 → 1666

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

RNA

NR_133670.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC114598, BC072650, CJ108618, CJ248638

Related

ENSMUST00000209735.2