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

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; 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, Apr 2022]
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

Location:: 19p13.3

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1269332..1274880)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (1237856..1243403)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1269331..1274879)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
MiR-383-5p promotes apoptosis of ovarian granulosa cells by targeting CIRP through the PI3K/AKT signaling pathway.
Title: MiR-383-5p promotes apoptosis of ovarian granulosa cells by targeting CIRP through the PI3K/AKT signaling pathway.
Downregulation of CIRP Prone Cells to Oxidative Injury via Regulating Nrf2 Signaling Pathway.
Title: Downregulation of CIRP Prone Cells to Oxidative Injury via Regulating Nrf2 Signaling Pathway.
CIRBP-OGFR axis safeguards against cardiomyocyte apoptosis and cardiotoxicity induced by chemotherapy.
Title: CIRBP-OGFR axis safeguards against cardiomyocyte apoptosis and cardiotoxicity induced by chemotherapy.

Submit: New GeneRIF Correction See all GeneRIFs (54)

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)

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

RH11815 (e-PCR)
- UniSTS:22669

IB1264 (e-PCR)
- UniSTS:77743

D19S683E (e-PCR)
- UniSTS:24020

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 more info	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)

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
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
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

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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

1269332..1274880

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

XR_001753600.3 RNA Sequence
XR_001753599.2 RNA Sequence

Related

ENST00000591376.5

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

1237856..1243403

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

K7EPM4
XM_054319714.1 → XP_054175689.1 cold-inducible RNA-binding protein isoform X1

UniProtKB/TrEMBL

K7EQR7
XM_054319715.1 → XP_054175690.1 cold-inducible RNA-binding protein isoform X2

UniProtKB/Swiss-Prot

B3KT17, B4E2X2, Q14011

UniProtKB/TrEMBL

Q53XX5