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CIRBP cold inducible RNA binding protein [ Homo sapiens (human) ]

Gene ID: 1153, updated on 13-Jan-2019

Summary

Official Symbol
CIRBPprovided by HGNC
Official Full Name
cold inducible RNA binding proteinprovided by HGNC
Primary source
HGNC:HGNC:1982
See related
Ensembl:ENSG00000099622 MIM:602649
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CIRP
Expression
Ubiquitous expression in ovary (RPKM 151.3), endometrium (RPKM 107.4) and 25 other tissues See more
Orthologs

Genomic context

See CIRBP in Genome Data Viewer
Location:
19p13.3
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (1269266..1274810)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1269267..1274809)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene midnolin Neighboring gene uncharacterized LOC107985303 Neighboring gene uncharacterized LOC105372236 Neighboring gene CIRBP antisense RNA 1 Neighboring gene chromosome 19 open reading frame 24 Neighboring gene ephrin A2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of cold inducible RNA binding protein (CIRBP) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(U) RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
small ribosomal subunit rRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
small ribosomal subunit rRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
translation repressor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
translation repressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
mRNA stabilization IDA
Inferred from Direct Assay
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
response to UV IDA
Inferred from Direct Assay
more info
PubMed 
response to cold IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
stress granule assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasmic stress granule ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
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
testicular tissue protein Li 39

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_001280.2NP_001271.1  cold-inducible RNA-binding protein isoform 1

    See identical proteins and their annotated locations for NP_001271.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) uses alternate splice sites at the 3' end, resulting in a novel 3' coding region and 3' UTR, compared to variant 5. It encodes isoform 1, which has a shorter and distinct C-terminus, compared to isoform 3.
    Source sequence(s)
    AF021336, BC000403, BP195090
    Consensus CDS
    CCDS12059.1
    UniProtKB/Swiss-Prot
    Q14011
    UniProtKB/TrEMBL
    Q53XX5
    Related
    ENSP00000322887.4, ENST00000320936.9
    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. NM_001300815.1NP_001287744.1  cold-inducible RNA-binding protein isoform 2

    See identical proteins and their annotated locations for NP_001287744.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 5. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 3.
    Source sequence(s)
    BC000403, BM706055, BU689520, DA695021
    Consensus CDS
    CCDS74244.1
    UniProtKB/Swiss-Prot
    Q14011
    UniProtKB/TrEMBL
    K7EPM4
    Related
    ENSP00000467848.1, ENST00000589235.5
    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. NM_001300829.2NP_001287758.1  cold-inducible RNA-binding protein isoform 3

    See identical proteins and their annotated locations for NP_001287758.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3).
    Source sequence(s)
    AC004258, AK094781, BC000403, DA433715
    Consensus CDS
    CCDS74245.1
    UniProtKB/Swiss-Prot
    Q14011
    UniProtKB/TrEMBL
    D6W5Y5
    Related
    ENSP00000466025.1, ENST00000587896.5
    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

RNA

  1. NR_023312.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice acceptor site for exon 2, represents an alternate 3'UTR and is a candidate for nonsense-mediated decay. Therefore, the CDS is not annotated on this record.
    Source sequence(s)
    AC004258, AL133636, BI819825, BP195090, CX785176
  2. NR_023313.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate exon resulting in a frameshift and premature truncation of the predicted protein. The transcript also represents an alternate 3'UTR and is a candidate for nonsense-mediated decay.
    Source sequence(s)
    AK094781, AL133636, BP195090
    Related
    ENST00000587169.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    1269266..1274810
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026237.2XP_016881726.1  cold-inducible RNA-binding protein isoform X3

    UniProtKB/TrEMBL
    K7EPM4
    Related
    ENSP00000468645.1, ENST00000586773.5
    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_011527668.1XP_011525970.1  cold-inducible RNA-binding protein isoform X1

    UniProtKB/TrEMBL
    K7EQR7
    Related
    ENSP00000467948.1, ENST00000585914.5
    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_006722637.2XP_006722700.1  cold-inducible RNA-binding protein isoform X2

    See identical proteins and their annotated locations for XP_006722700.1

    UniProtKB/Swiss-Prot
    Q14011
    UniProtKB/TrEMBL
    Q53XX5
    Related
    ENSP00000466110.1, ENST00000585630.5
    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

RNA

  1. XR_001753600.2 RNA Sequence

  2. XR_001753598.1 RNA Sequence

  3. XR_001753599.1 RNA Sequence

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