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

Gene ID: 12826, updated on 1-Mar-2024

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
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Genomic context

See Col4a1 in Genome Data Viewer
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_000074.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 9530052E02 gene Neighboring gene STARR-positive B cell enhancer ABC_E3768 Neighboring gene insulin receptor substrate 2 Neighboring gene predicted gene 44717 Neighboring gene predicted gene 15418 Neighboring gene predicted gene, 32709 Neighboring gene collagen, type IV, alpha 2 Neighboring gene predicted gene, 46030 Neighboring gene STARR-seq mESC enhancer starr_20711 Neighboring gene predicted gene 15419

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 
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 PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region TAS
Traceable Author Statement
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

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)

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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)

  1. NM_009931.2NP_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:10881147
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15561666
    C4; C-terminal tandem repeated domain in type 4 procollagen

RNA

  1. 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

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

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    11248423..11362889 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_004934755.1 RNA Sequence