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Col4a4 collagen, type IV, alpha 4 [ Mus musculus (house mouse) ]

Gene ID: 12829, updated on 18-Apr-2019

Summary

Official Symbol
Col4a4provided by MGI
Official Full Name
collagen, type IV, alpha 4provided by MGI
Primary source
MGI:MGI:104687
See related
Ensembl:ENSMUSG00000067158
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]4(IV); E130010M05Rik
Expression
Biased expression in kidney adult (RPKM 12.0), lung adult (RPKM 10.4) and 6 other tissues See more
Orthologs

Genomic context

See Col4a4 in Genome Data Viewer
Location:
1; 1 C5
Exon count:
50
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 1 NC_000067.6 (82448419..82586927, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (82447298..82583424, complement)

Chromosome 1 - NC_000067.6Genomic Context describing neighboring genes Neighboring gene insulin receptor substrate 1 Neighboring gene rhomboid domain containing 1 Neighboring gene predicted gene, 46095 Neighboring gene collagen, type IV, alpha 3 Neighboring gene RIKEN cDNA C430014B12 gene Neighboring gene predicted gene, 39668 Neighboring gene mitochondrial fission factor

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 FunctionsWhat's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Spontaneous (1)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (1) 

Pathways from BioSystems

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent IPI
Inferred from Physical Interaction
more info
PubMed 
extracellular matrix structural constituent ISO
Inferred from Sequence Orthology
more info
 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
Process Evidence Code Pubs
angiogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endothelial cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glomerular basement membrane development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glomerular basement membrane development IMP
Inferred from Mutant Phenotype
more info
PubMed 
glomerular basement membrane development ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
basement membrane ISO
Inferred from Sequence Orthology
more info
 
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
collagen type IV trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IV trimer IDA
Inferred from Direct Assay
more info
PubMed 
collagen type IV trimer ISO
Inferred from Sequence Orthology
more info
 
collagen-containing extracellular matrix HDA PubMed 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-4(IV) chain
Names
col4a4
procollagen, type IV, alpha 4

NCBI Reference Sequences (RefSeq)

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_007735.2NP_031761.1  collagen alpha-4(IV) chain precursor

    See identical proteins and their annotated locations for NP_031761.1

    Status: VALIDATED

    Source sequence(s)
    AC160543, AF169388, AK164732
    Consensus CDS
    CCDS35630.1
    UniProtKB/Swiss-Prot
    Q9QZR9
    Related
    ENSMUSP00000084282.5, ENSMUST00000087050.6
    Conserved Domains (2) summary
    pfam01391
    Location:54111
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14581562
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000067.6 Reference GRCm38.p4 C57BL/6J

    Range
    82448419..82586927 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011238652.1XP_011236954.1  collagen alpha-4(IV) chain isoform X1

    Conserved Domains (2) summary
    pfam01391
    Location:792851
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:13611465
    C4; C-terminal tandem repeated domain in type 4 procollagen
  2. XM_011238653.2XP_011236955.1  collagen alpha-4(IV) chain isoform X2

    Conserved Domains (1) summary
    pfam01391
    Location:54111
    Collagen; Collagen triple helix repeat (20 copies)
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