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

Gene ID: 1153, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:1982
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
Summary
Enables mRNA 3'-UTR binding activity and small ribosomal subunit rRNA binding activity. Involved in mRNA stabilization; positive regulation of translation; and response to UV. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 151.3), endometrium (RPKM 107.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See CIRBP in Genome Data Viewer
Location:
19p13.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1269332..1274880)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1237856..1243403)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1269331..1274879)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1248659-1249192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9677 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1251037-1251976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9688 Neighboring gene midnolin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9690 Neighboring gene IQ motif and SEC7 domain-containing protein 2-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13604 Neighboring gene uncharacterized LOC105372236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9694 Neighboring gene CIRBP antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9695 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1273486-1273669 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1275036-1275260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13608 Neighboring gene family with sequence similarity 174 member C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1282586-1283432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1284956-1285456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1285457-1285957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1287962-1288548 Neighboring gene ephrin A2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1291327-1292207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1293760-1294329

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. The Cold-Inducible RNA-Binding Protein (CIRP) Level in Peripheral Blood Predicts Sepsis Outcome. Zhou Y, et al. PLoS One, 2015. PMID 26361390, Free PMC Article
  2. CIRBP Regulates Pancreatic Cancer Cell Ferroptosis and Growth by Directly Binding to p53. Gao H, et al. J Immunol Res, 2022. PMID 36061308, Free PMC Article
  3. Serum and synovial fluid concentrations of cold-inducible RNA-binding protein in patients with rheumatoid arthritis. Yoo IS, et al. Int J Rheum Dis, 2018 Jan. PMID 27315340
  4. Cold-inducible RNA binding protein regulates mucin expression induced by cold temperatures in human airway epithelial cells. Ran D, et al. Arch Biochem Biophys, 2016 Aug 1. PMID 27184164
  5. Heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by increasing protein translation of selected transcripts in cancer cells. Chang ET, et al. Oncotarget, 2016 Mar 1. PMID 26824423, Free PMC Article

See all (168) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genomic analysis uncovers that cold-inducible RNA binding protein is associated with estrogen receptor in breast cancer.
    Title: Genomic analysis uncovers that cold-inducible RNA binding protein is associated with estrogen receptor in breast cancer.
  2. BMAL2 promotes eCIRP-induced macrophage endotoxin tolerance.
    Title: BMAL2 promotes eCIRP-induced macrophage endotoxin tolerance.
  3. Extracellular CIRP co-stimulated T cells through IL6R/STAT3 in pediatric IgA vasculitis.
    Title: Extracellular CIRP co-stimulated T cells through IL6R/STAT3 in pediatric IgA vasculitis.
  4. Circulating cold-inducible RNA-binding protein levels in microscopic polyangiitis and granulomatosis with polyangiitis : Correlation with disease activity.
    Title: Circulating cold-inducible RNA-binding protein levels in microscopic polyangiitis and granulomatosis with polyangiitis : Correlation with disease activity.
  5. Extracellular CIRP induces abnormal activation of fibroblast-like synoviocytes from patients with RA via the TLR4-mediated HDAC3 pathways.
    Title: Extracellular CIRP induces abnormal activation of fibroblast-like synoviocytes from patients with RA via the TLR4-mediated HDAC3 pathways.
  6. The effect of HYPE knock-out on the AMPylome of human OSU-CLL leukemia cells.
    Title: The effect of HYPE knock-out on the AMPylome of human OSU-CLL leukemia cells.
  7. Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection.
    Title: Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection.
  8. Serum cold-inducible RNA-binding protein levels as a potential biomarker for systemic sclerosis-associated interstitial lung disease.
    Title: Serum cold-inducible RNA-binding protein levels as a potential biomarker for systemic sclerosis-associated interstitial lung disease.
  9. ETS-1 facilitates Th1 cell-mediated mucosal inflammation in inflammatory bowel diseases through upregulating CIRBP.
    Title: ETS-1 facilitates Th1 cell-mediated mucosal inflammation in inflammatory bowel diseases through upregulating CIRBP.
  10. CIRBP Regulates Pancreatic Cancer Cell Ferroptosis and Growth by Directly Binding to p53.
    Title: CIRBP Regulates Pancreatic Cancer Cell Ferroptosis and Growth by Directly Binding to p53.
Submit: New GeneRIF Correction See all GeneRIFs (57)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small ribosomal subunit rRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables translation repressor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in mRNA stabilization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of translation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of translation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to cold TAS
Traceable Author Statement
more info
 PubMed 
involved_in stress granule assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasmic stress granule ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus HDA PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
cold-inducible RNA-binding protein
Names
A18 hnRNP
glycine-rich RNA binding protein
testicular tissue protein Li 39

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_001280.3 → NP_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
    B3KT17, B4E2X2, Q14011
    UniProtKB/TrEMBL
    K7EMY9, Q53XX5
    Related
    ENSP00000322887.4, ENST00000320936.9
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

  2. NM_001300815.2 → NP_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/TrEMBL
    K7EMY9, K7EPM4
    Related
    ENSP00000467848.1, ENST00000589235.5
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

  3. NM_001300829.2 → NP_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/TrEMBL
    D6W5Y5
    Related
    ENSP00000466025.1, ENST00000587896.6
    Conserved Domains (2) summary
    COG0724
    Location:3 → 90
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12449
    Location:6 → 85
    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_023312.3 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_023313.3 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)
    AC004258, AK094781, AL133636, BP195090
    Related
    ENST00000587169.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    1269332..1274880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    K7EMY9, K7EPM4
    Related
    ENSP00000468645.1, ENST00000586773.5
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

  2. XM_011527668.1 → XP_011525970.1  cold-inducible RNA-binding protein isoform X1

    UniProtKB/TrEMBL
    K7EQR7
    Related
    ENSP00000467948.1, ENST00000585914.5
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

  3. XM_006722637.2 → XP_006722700.1  cold-inducible RNA-binding protein isoform X2

    See identical proteins and their annotated locations for XP_006722700.1

    UniProtKB/Swiss-Prot
    B3KT17, B4E2X2, Q14011
    UniProtKB/TrEMBL
    K7EMY9, Q53XX5
    Related
    ENSP00000466110.1, ENST00000585630.5
    Conserved Domains (1) summary
    cd12449
    Location:6 → 85
    RRM_CIRBP_RBM3; RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

RNA

  1. XR_001753600.3 RNA Sequence

  2. XR_001753599.2 RNA Sequence

    Related
    ENST00000591376.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    1237856..1243403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319716.1 → XP_054175691.1  cold-inducible RNA-binding protein isoform X3

    UniProtKB/TrEMBL
    K7EPM4

  2. XM_054319714.1 → XP_054175689.1  cold-inducible RNA-binding protein isoform X1

    UniProtKB/TrEMBL
    K7EQR7

  3. XM_054319715.1 → XP_054175690.1  cold-inducible RNA-binding protein isoform X2

    UniProtKB/Swiss-Prot
    B3KT17, B4E2X2, Q14011
    UniProtKB/TrEMBL
    Q53XX5

RNA

  1. XR_008485080.1 RNA Sequence

  2. XR_008485079.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14011.1 GenPept UniProtKB/Swiss-Prot:Q14011

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