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Aliases for CIRBP Gene

Aliases for CIRBP Gene

  • Cold Inducible RNA Binding Protein 2 3 5
  • Cold-Inducible RNA-Binding Protein 2 3
  • Glycine-Rich RNA Binding Protein 2 3
  • A18 HnRNP 3 4
  • CIRP 3 4
  • Glycine-Rich RNA-Binding Protein CIRP 4
  • Cold Inducible RNA-Binding Protein 2
  • Testicular Tissue Protein Li 39 3
  • A18HNRNP 4

External Ids for CIRBP Gene

Previous GeneCards Identifiers for CIRBP Gene

  • GC19P001327
  • GC19P001209
  • GC19P001220
  • GC19P001044

Summaries for CIRBP Gene

GeneCards Summary for CIRBP Gene

CIRBP (Cold Inducible RNA Binding Protein) is a Protein Coding gene. Diseases associated with CIRBP include Cryptorchidism, Unilateral Or Bilateral. Among its related pathways are Translational Control and Neuroscience. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is RBMX.

UniProtKB/Swiss-Prot for CIRBP Gene

  • Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold-induced suppression of cell proliferation. Binds specifically to the 3-untranslated regions (3-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor (By similarity). Promotes assembly of stress granules (SGs), when overexpressed.

Gene Wiki entry for CIRBP Gene

Additional gene information for CIRBP Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CIRBP Gene

Genomics for CIRBP Gene

GeneHancer (GH) Regulatory Elements for CIRBP Gene

Promoters and enhancers for CIRBP Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J001236 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 741.9 -2.5 -2525 41.1 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 CIRBP C19orf24 MIDN CBARP ATP5F1D SF3A2 TCF3 TMEM259 LOC100288123 MIER2
GH19J001382 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 135.6 +124.6 124642 2.2 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NDUFS7 TRF-GAA1-6 TRN-GTT2-6 PIR60227 PIR43938 SF3A2 CIRBP TMEM259 DAZAP1 LOC100288123
GH19J001202 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 102.4 -52.6 -52627 8 ZFP64 FEZF1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A STK11 CIRBP TMEM259 DAZAP1 LOC100288123 TCF3 PTBP1 GRIN3B DOT1L POLRMT
GH19J001097 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 55 -153.3 -153318 17 MLX DMAP1 IRF4 YY1 ZNF143 SP3 NFYC SSRP1 GLIS1 RCOR2 GPX4 GC19P001106 GC19P001105 CIRBP TMEM259 LOC100288123 DAZAP1 TCF3 PTBP1 GRIN3B
GH19J001019 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 60.4 -238.2 -238177 4.4 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 TMEM259 RNU6-2 GC19P001025 DAZAP1 LOC100288123 TCF3 GRIN3B PTBP1 MED16 CIRBP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CIRBP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CIRBP gene promoter:

Genomic Locations for CIRBP Gene

Genomic Locations for CIRBP Gene
chr19:1,259,384-1,274,880
(GRCh38/hg38)
Size:
15,497 bases
Orientation:
Plus strand
chr19:1,259,384-1,274,879
(GRCh37/hg19)

Genomic View for CIRBP Gene

Genes around CIRBP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CIRBP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CIRBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CIRBP Gene

Proteins for CIRBP Gene

  • Protein details for CIRBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14011-CIRBP_HUMAN
    Recommended name:
    Cold-inducible RNA-binding protein
    Protein Accession:
    Q14011
    Secondary Accessions:
    • B3KT17
    • B4E2X2

    Protein attributes for CIRBP Gene

    Size:
    172 amino acids
    Molecular mass:
    18648 Da
    Quaternary structure:
    • Interacts with EIF4G1. Associates with ribosomes.

    Three dimensional structures from OCA and Proteopedia for CIRBP Gene

    Alternative splice isoforms for CIRBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CIRBP Gene

Post-translational modifications for CIRBP Gene

  • Methylated on arginine residues. Methylation of the RGG motifs is a prerequisite for recruitment into SGs (By similarity).
  • Phosphorylated by CK2, GSK3A and GSK3B. Phosphorylation by GSK3B increases RNA-binding activity to the TXN 3-UTR transcript upon exposure to UV radiation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CIRBP Gene

Domains & Families for CIRBP Gene

Gene Families for CIRBP Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

Q14011

UniProtKB/Swiss-Prot:

CIRBP_HUMAN :
  • Both the RRM domain and the arginine, glycine (RGG) rich domain are necessary for binding to the TXN 3-untranslated region. Both the RRM domain and the arginine, glycine (RGG) rich domain (RGG repeats) are necessary for optimal recruitment into SGs upon cellular stress. The C-terminal domain containing RGG repeats is necessary for translational repression (By similarity).
Domain:
  • Both the RRM domain and the arginine, glycine (RGG) rich domain are necessary for binding to the TXN 3-untranslated region. Both the RRM domain and the arginine, glycine (RGG) rich domain (RGG repeats) are necessary for optimal recruitment into SGs upon cellular stress. The C-terminal domain containing RGG repeats is necessary for translational repression (By similarity).
genes like me logo Genes that share domains with CIRBP: view

Function for CIRBP Gene

Molecular function for CIRBP Gene

UniProtKB/Swiss-Prot Function:
Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold-induced suppression of cell proliferation. Binds specifically to the 3-untranslated regions (3-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor (By similarity). Promotes assembly of stress granules (SGs), when overexpressed.
UniProtKB/Swiss-Prot Induction:
By cold stress in response to DNA damage induced by UV irradiation or UV mimetic agents. Up-regulated by hypoxia.
GENATLAS Biochemistry:
cold inducible RNA binding-protein,18kDa,ubiquitously expressed,mouse Cirp homolog

Phenotypes From GWAS Catalog for CIRBP Gene

Gene Ontology (GO) - Molecular Function for CIRBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,HDA 22658674
GO:0003730 mRNA 3-UTR binding IDA 11574538
GO:0005515 protein binding IPI 16189514
GO:0030371 translation repressor activity ISS --
GO:0070181 small ribosomal subunit rRNA binding IDA 11574538
genes like me logo Genes that share ontologies with CIRBP: view
genes like me logo Genes that share phenotypes with CIRBP: view

Animal Models for CIRBP Gene

MGI Knock Outs for CIRBP:

Animal Model Products

miRNA for CIRBP Gene

miRTarBase miRNAs that target CIRBP

Clone Products

  • Addgene plasmids for CIRBP

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CIRBP Gene

Localization for CIRBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for CIRBP Gene

Nucleus, nucleoplasm. Cytoplasm. Note=Translocates from the nucleus to the cytoplasm after exposure to UV radiation. Translocates from the nucleus to the cytoplasm into stress granules upon various cytoplasmic stresses, such as osmotic and heat shocks. Its recruitment into stress granules occurs in the absence of TIAR proteins (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CIRBP gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CIRBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,ISS --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm ISS --
GO:0010494 cytoplasmic stress granule ISS --
genes like me logo Genes that share ontologies with CIRBP: view

Pathways & Interactions for CIRBP Gene

genes like me logo Genes that share pathways with CIRBP: view

Pathways by source for CIRBP Gene

3 Cell Signaling Technology pathways for CIRBP Gene

Gene Ontology (GO) - Biological Process for CIRBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009409 response to cold TAS 9151692
GO:0009411 response to UV IDA 11574538
GO:0017148 negative regulation of translation IEA --
GO:0034063 stress granule assembly ISS --
GO:0045727 positive regulation of translation IDA 11574538
genes like me logo Genes that share ontologies with CIRBP: view

No data available for SIGNOR curated interactions for CIRBP Gene

Drugs & Compounds for CIRBP Gene

(3) Additional Compounds for CIRBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CIRBP: view

Transcripts for CIRBP Gene

Unigene Clusters for CIRBP Gene

Cold inducible RNA binding protein:
Representative Sequences:

Clone Products

  • Addgene plasmids for CIRBP

Alternative Splicing Database (ASD) splice patterns (SP) for CIRBP Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11
SP1: - - - - - - - - -
SP2: - - -
SP3: -
SP4: - -
SP5: - - - - -
SP6: - - - - - -
SP7: - -
SP8: -

Relevant External Links for CIRBP Gene

GeneLoc Exon Structure for
CIRBP
ECgene alternative splicing isoforms for
CIRBP

Expression for CIRBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CIRBP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CIRBP Gene

This gene is overexpressed in Nasal epithelium (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CIRBP Gene



Protein tissue co-expression partners for CIRBP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CIRBP Gene:

CIRBP

SOURCE GeneReport for Unigene cluster for CIRBP Gene:

Hs.618145

mRNA Expression by UniProt/SwissProt for CIRBP Gene:

Q14011-CIRBP_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for CIRBP Gene

  • Nervous system(5)
  • Lung(4.8)
  • Liver(4.5)
  • Eye(4.2)
  • Pancreas(3.8)
  • Intestine(3.2)
  • Kidney(3)
  • Spleen(2.9)
  • Heart(2.7)
  • Skin(2.5)
  • Lymph node(2.3)
  • Thyroid gland(2.3)
  • Adrenal gland(2.2)
  • Bone marrow(2.2)
  • Muscle(2.2)
  • Stomach(2.2)
  • Gall bladder(2.1)
genes like me logo Genes that share expression patterns with CIRBP: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for CIRBP Gene

Orthologs for CIRBP Gene

This gene was present in the common ancestor of animals.

Orthologs for CIRBP Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia CIRBP 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CIRBP 34 33
  • 91.09 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CIRBP 34 33
  • 90.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Cirbp 16 34 33
  • 86.63 (n)
rat
(Rattus norvegicus)
Mammalia Cirbp 33
  • 85.08 (n)
chimpanzee
(Pan troglodytes)
Mammalia CIRBP 34 33
  • 83.18 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CIRBP 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves CIRBP 34 33
  • 82.44 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CIRBP 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cirbp 33
  • 71.17 (n)
African clawed frog
(Xenopus laevis)
Amphibia cirbp-prov 33
zebrafish
(Danio rerio)
Actinopterygii cirbpa 33
  • 61.01 (n)
CIRBP (2 of 2) 34
  • 58 (a)
OneToMany
cirbp 34
  • 54 (a)
OneToMany
wufb74g05 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3932 33
fruit fly
(Drosophila melanogaster)
Insecta tra2 34
  • 16 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rsp-8 34
  • 19 (a)
OneToMany
Species where no ortholog for CIRBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CIRBP Gene

ENSEMBL:
Gene Tree for CIRBP (if available)
TreeFam:
Gene Tree for CIRBP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CIRBP: view image

Paralogs for CIRBP Gene

(55) SIMAP similar genes for CIRBP Gene using alignment to 18 proteins:

  • CIRBP_HUMAN
  • B3KT17_HUMAN
  • B4E2X2_HUMAN
  • D6W5Y5_HUMAN
  • K7EIF7_HUMAN
  • K7EJV5_HUMAN
  • K7ELL4_HUMAN
  • K7ELT6_HUMAN
  • K7ELV6_HUMAN
  • K7EMY9_HUMAN
  • K7ENN6_HUMAN
  • K7ENX8_HUMAN
  • K7EPM4_HUMAN
  • K7EQL0_HUMAN
  • K7EQR7_HUMAN
  • K7EQX4_HUMAN
  • K7ER40_HUMAN
  • Q53XX5_HUMAN
genes like me logo Genes that share paralogs with CIRBP: view

Variants for CIRBP Gene

Sequence variations from dbSNP and Humsavar for CIRBP Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000552140 -- 1,269,140(+) G/A upstream_transcript_variant
rs1000665216 -- 1,268,990(+) C/T upstream_transcript_variant
rs1001184541 -- 1,272,547(+) C/T 3_prime_UTR_variant, intron_variant, non_coding_transcript_variant
rs1001218200 -- 1,271,878(+) C/T intron_variant
rs1001274601 -- 1,272,644(+) G/C 3_prime_UTR_variant, intron_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CIRBP Gene

Variant ID Type Subtype PubMed ID
dgv136n111 CNV deletion 26073780
esv2758743 CNV gain+loss 17122850
esv3643389 CNV gain 21293372
esv3643390 CNV loss 21293372
esv3643391 CNV gain 21293372
nsv1055164 CNV gain 25217958
nsv1058677 CNV loss 25217958
nsv1060536 CNV gain 25217958
nsv1160555 CNV deletion 26073780
nsv470103 CNV gain 18288195
nsv470104 CNV loss 18288195
nsv828368 CNV gain 20364138
nsv828371 CNV loss 20364138
nsv953941 CNV deletion 24416366
nsv9662 CNV gain 18304495

Variation tolerance for CIRBP Gene

Residual Variation Intolerance Score: 36.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CIRBP Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CIRBP

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CIRBP Gene

Disorders for CIRBP Gene

MalaCards: The human disease database

(1) MalaCards diseases for CIRBP Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
cryptorchidism, unilateral or bilateral
  • undescended testis
- elite association - COSMIC cancer census association via MalaCards
Search CIRBP in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CIRBP

genes like me logo Genes that share disorders with CIRBP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CIRBP Gene

Publications for CIRBP Gene

  1. Cloning and characterization of human CIRP (cold-inducible RNA-binding protein) cDNA and chromosomal assignment of the gene. (PMID: 9434172) Nishiyama H … Fujita J (Gene 1997) 2 3 4 22 58
  2. Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism. (PMID: 15075239) Wellmann S … Seeger K (Journal of cell science 2004) 3 4 22 58
  3. The UV-inducible RNA-binding protein A18 (A18 hnRNP) plays a protective role in the genotoxic stress response. (PMID: 11574538) Yang C … Carrier F (The Journal of biological chemistry 2001) 3 4 22 58
  4. Cold-inducible RNA-binding protein bypasses replicative senescence in primary cells through extracellular signal-regulated kinase 1 and 2 activation. (PMID: 19158277) Artero-Castro A … Lleonart ME (Molecular and cellular biology 2009) 3 22 58
  5. Down-regulating cold shock protein genes impairs cancer cell survival and enhances chemosensitivity. (PMID: 19277990) Zeng Y … Getzenberg RH (Journal of cellular biochemistry 2009) 3 22 58

Products for CIRBP Gene