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Cirbp cold inducible RNA binding protein [ Rattus norvegicus (Norway rat) ]

Gene ID: 81825, updated on 10-Oct-2019

Summary

Official Symbol
Cirbpprovided by RGD
Official Full Name
cold inducible RNA binding proteinprovided by RGD
Primary source
RGD:620756
See related
Ensembl:ENSRNOG00000015999
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
expression decreased by ischemia and H2O2; may mediate generation of reactive oxygen species [RGD, Feb 2006]
Expression
Biased expression in Lung (RPKM 236.7), Adrenal (RPKM 202.3) and 9 other tissues See more
Orthologs

Genomic context

See Cirbp in Genome Data Viewer
Location:
7q11
Exon count:
8
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (12400066..12405054, complement)
106 current Rn_Celera (GCF_000002265.2) 7 AC_000075.1 (7711175..7714992, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 7 NC_005106.3 (12570171..12575155, complement)

Chromosome 7 - NC_005106.4Genomic Context describing neighboring genes Neighboring gene ephrin A2 Neighboring gene homeobox protein MIXL1-like Neighboring gene family with sequence similarity 174 member C Neighboring gene midnolin Neighboring gene ATP synthase F1 subunit delta

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?

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
mRNA 3'-UTR binding ISO
Inferred from Sequence Orthology
more info
PubMed 
mRNA 3'-UTR binding ISS
Inferred from Sequence or Structural Similarity
more info
 
poly(U) RNA binding IEA
Inferred from Electronic Annotation
more info
 
poly(U) RNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
small ribosomal subunit rRNA binding ISO
Inferred from Sequence Orthology
more info
PubMed 
small ribosomal subunit rRNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
translation repressor activity ISO
Inferred from Sequence Orthology
more info
PubMed 
translation repressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
cellular response to cold IEA
Inferred from Electronic Annotation
more info
 
cellular response to cold ISO
Inferred from Sequence Orthology
more info
PubMed 
mRNA stabilization ISO
Inferred from Sequence Orthology
more info
PubMed 
mRNA stabilization ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell growth ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of translation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of translation ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell cycle G1/S phase transition IEA
Inferred from Electronic Annotation
more info
 
regulation of cell cycle G1/S phase transition ISO
Inferred from Sequence Orthology
more info
PubMed 
response to UV ISO
Inferred from Sequence Orthology
more info
PubMed 
response to UV ISS
Inferred from Sequence or Structural Similarity
more info
 
response to cold IEP
Inferred from Expression Pattern
more info
PubMed 
stress granule assembly ISO
Inferred from Sequence Orthology
more info
PubMed 
stress granule assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm ISO
Inferred from Sequence Orthology
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasmic stress granule ISO
Inferred from Sequence Orthology
more info
PubMed 
cytoplasmic stress granule ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
cold-inducible RNA-binding protein
Names
A18 hnRNP
glycine-rich RNA-binding protein CIRP

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_031147.2NP_112409.2  cold-inducible RNA-binding protein

    See identical proteins and their annotated locations for NP_112409.2

    Status: PROVISIONAL

    Source sequence(s)
    BC069219
    UniProtKB/TrEMBL
    Q6NT88
    Related
    ENSRNOP00000021648.4, ENSRNOT00000021648.6
    Conserved Domains (2) summary
    COG0724
    Location:390
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

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_005106.4 Reference Rnor_6.0 Primary Assembly

    Range
    12400066..12405054 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_008765132.2XP_008763354.2  cold-inducible RNA-binding protein isoform X3

    Conserved Domains (1) summary
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  2. XM_006241015.3XP_006241077.3  cold-inducible RNA-binding protein isoform X2

    UniProtKB/Swiss-Prot
    P60825
    Conserved Domains (1) summary
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  3. XM_017595131.1XP_017450620.1  cold-inducible RNA-binding protein isoform X1

    Conserved Domains (2) summary
    COG0724
    Location:390
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  4. XM_006241013.3XP_006241075.3  cold-inducible RNA-binding protein isoform X1

    Conserved Domains (2) summary
    COG0724
    Location:390
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  5. XM_017595132.1XP_017450621.1  cold-inducible RNA-binding protein isoform X3

    Conserved Domains (1) summary
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  6. XM_006241014.3XP_006241076.1  cold-inducible RNA-binding protein isoform X2

    See identical proteins and their annotated locations for XP_006241076.1

    UniProtKB/Swiss-Prot
    P60825
    Conserved Domains (1) summary
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins
  7. XM_006241012.3XP_006241074.1  cold-inducible RNA-binding protein isoform X1

    See identical proteins and their annotated locations for XP_006241074.1

    Conserved Domains (2) summary
    COG0724
    Location:390
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12449
    Location:685
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

Alternate Rn_Celera

Genomic

  1. AC_000075.1 Alternate Rn_Celera

    Range
    7711175..7714992 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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