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Col4a1 collagen type IV alpha 1 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 290905, updated on 5-Jan-2022

Summary

Official Symbol
Col4a1provided by RGD
Official Full Name
collagen type IV alpha 1 chainprovided by RGD
Primary source
RGD:1307148
See related
Ensembl:ENSRNOG00000016281
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable platelet-derived growth factor binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in epithelial cell differentiation. Predicted to be located in extracellular region. Predicted to be part of collagen type IV trimer. Predicted to be active in basement membrane and extracellular space. Biomarker of pulmonary hypertension. Human ortholog(s) of this gene implicated in brain small vessel disease 1; myocardial infarction; and retinal arterial tortuosity. Orthologous to human COL4A1 (collagen type IV alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2021]
Expression
Biased expression in Lung (RPKM 831.5), Kidney (RPKM 806.3) and 9 other tissues See more
Orthologs
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Genomic context

See Col4a1 in Genome Data Viewer
Location:
16q12.5
Exon count:
52
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 16 NC_051351.1 (78183533..78294412)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 16 NC_005115.4 (83522162..83632153)

Chromosome 16 - NC_051351.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102553902 Neighboring gene RAB20, member RAS oncogene family Neighboring gene collagen type IV alpha 2 chain Neighboring gene uncharacterized LOC120097569 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase-like Neighboring gene uncharacterized LOC120097570

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix structural constituent ISO
Inferred from Sequence Orthology
more info
 
enables extracellular matrix structural constituent conferring tensile strength ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
more info
 
enables platelet-derived growth factor binding 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
PubMed 
located_in basement membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in cellular_component ND
No biological Data available
more info
 
part_of collagen type IV trimer ISO
Inferred from Sequence Orthology
more info
 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
collagen alpha-1(IV) chain
Names
alpha 1 type IV collagen
collagen, type IV, alpha 1
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_001135009.1NP_001128481.1  collagen alpha-1(IV) chain precursor

    Status: PROVISIONAL

    Source sequence(s)
    JACYVU010000283
    UniProtKB/TrEMBL
    F1MA59
    Related
    ENSRNOP00000054197.2, ENSRNOT00000057386.3
    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

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051351.1 Reference mRatBN7.2 Primary Assembly

    Range
    78183533..78294412
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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