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Col4a3 collagen type IV alpha 3 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 363265, updated on 18-Apr-2019

Summary

Official Symbol
Col4a3provided by RGD
Official Full Name
collagen type IV alpha 3 chainprovided by RGD
Primary source
RGD:71085
See related
Ensembl:ENSRNOG00000015365
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
autoimmunity to the NC1 domain of the human homolog causes the antiglomerular basement membrane (anti-GBM) disease [RGD, Feb 2006]
Expression
Biased expression in Kidney (RPKM 688.0), Lung (RPKM 331.8) and 4 other tissues See more
Orthologs

Genomic context

See Col4a3 in Genome Data Viewer
Location:
9q34
Exon count:
52
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (88357528..88484735)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 9 NC_005108.3 (88104667..88233491)

Chromosome 9 - NC_005108.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108351962 Neighboring gene rhomboid domain containing 1 Neighboring gene collagen type IV alpha 4 chain Neighboring gene uncharacterized LOC102554007 Neighboring gene uncharacterized LOC103693235 Neighboring gene mitochondrial fission factor Neighboring gene transmembrane 4 L six family member 20

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, organism-specific biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • AGE-RAGE signaling pathway in diabetic complications, conserved biosystem (from KEGG)
    AGE-RAGE signaling pathway in diabetic complications, conserved biosystemAdvanced glycation end products (AGEs) are a complex group of compounds produced through the non-enzymatic glycation and oxidation of proteins, lipids and nucleic acids, primarily due to aging and un...
  • Amoebiasis, organism-specific biosystem (from KEGG)
    Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Amoebiasis, conserved biosystem (from KEGG)
    Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Pathways in cancer, organism-specific biosystem (from KEGG)
    Pathways in cancer, organism-specific biosystem
    Pathways in cancer
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Small cell lung cancer, organism-specific biosystem (from KEGG)
    Small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Small cell lung cancer, conserved biosystem (from KEGG)
    Small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integrin binding IEA
Inferred from Electronic Annotation
more info
 
integrin binding ISO
Inferred from Sequence Orthology
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity involved in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
activation of cysteine-type endopeptidase activity involved in apoptotic process ISO
Inferred from Sequence Orthology
more info
PubMed 
cell proliferation IEA
Inferred from Electronic Annotation
more info
 
cell proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
cell surface receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen-activated tyrosine kinase receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
collagen-activated tyrosine kinase receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
PubMed 
endothelial cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
endothelial cell apoptotic process ISO
Inferred from Sequence Orthology
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glomerular basement membrane development IEA
Inferred from Electronic Annotation
more info
 
glomerular basement membrane development ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of angiogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
notochord development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to glucose IEP
Inferred from Expression Pattern
more info
PubMed 
skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
basement membrane ISO
Inferred from Sequence Orthology
more info
PubMed 
cellular_component ND
No biological Data available
more info
 
collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IV trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type IV trimer ISO
Inferred from Sequence Orthology
more info
PubMed 
collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
collagen alpha-3(IV) chain
Names
collagen, type IV, alpha 3 (Goodpasture antigen)
procollagen, type IV, alpha 3

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_001135759.1NP_001129231.1  collagen alpha-3(IV) chain precursor

    Status: PROVISIONAL

    Source sequence(s)
    AABR07068184, AABR07068185
    Conserved Domains (2) summary
    pfam01391
    Location:9781035
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14461552
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: Rattus norvegicus 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 Rnor_6.0 Primary Assembly

Genomic

  1. NC_005108.4 Reference Rnor_6.0 Primary Assembly

    Range
    88357528..88484735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245259.3XP_006245321.1  collagen alpha-3(IV) chain isoform X1

    UniProtKB/TrEMBL
    F1LRJ1
    Related
    ENSRNOP00000020669.5, ENSRNOT00000020669.5
    Conserved Domains (2) summary
    pfam01391
    Location:9791036
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14471553
    C4; C-terminal tandem repeated domain in type 4 procollagen

Alternate Rn_Celera

Genomic

  1. AC_000077.1 Alternate Rn_Celera

    Range
    81318911..81443381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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