Human Gene CIRBP (ENST00000587896.6_5) from GENCODE V47lift37

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Description: cold inducible RNA binding protein, transcript variant 2 (from RefSeq NR_023312.3)
Gencode Transcript: ENST00000587896.6_5
Gencode Gene: ENSG00000099622.14_15
Transcript (Including UTRs)
Position: hg19 chr19:1,269,331-1,274,809 Size: 5,479 Total Exon Count: 6 Strand: +
Coding Region
Position: hg19 chr19:1,270,933-1,272,442 Size: 1,510 Coding Exon Count: 5

Page Index	Sequence and Links	Primers	MalaCards	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr19:1,269,331-1,274,809)			mRNA (may differ from genome)		Protein (297 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	UniProtKB
Wikipedia	BioGrid CRISPR DB

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: CIRBP Diseases sorted by gene-association score: cryptorchidism (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen D019256 Cadmium Chloride D019327 Copper Sulfate C006780 bisphenol A C025589 ochratoxin A C023036 perfluorooctanoic acid D015058 1-Naphthylisothiocyanate D015085 2,4,5-Trichlorophenoxyacetic Acid C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone C009505 4,4'-diaminodiphenylmethane C035207 4-amino-2,6-dinitrotoluene D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide C547126 AZM551248 D000086 Acetazolamide D000393 Air Pollutants D000452 Aldrin D000643 Ammonium Chloride D001564 Benzo(a)pyrene D002258 Carbonyl Cyanide m-Chlorophenyl Hydrazone D002737 Chloroprene D002922 Ciguatoxins D002994 Clofibrate D003907 Dexamethasone D004041 Dietary Fats D004147 Dioxins D004958 Estradiol D000431 Ethanol D004997 Ethinyl Estradiol D007545 Isoproterenol D008070 Lipopolysaccharides D008344 Maneb D008767 Methylmercury Compounds D009020 Morphine D009538 Nicotine D010126 Ozone D010269 Paraquat D011078 Polychlorinated Biphenyls D011794 Quercetin D012402 Rotenone D019810 Sodium Azide C041711 St. Thomas' Hospital cardioplegic solution D013629 Tamoxifen D013749 Tetrachlorodibenzodioxin D013759 Tetrahydrocannabinol D014241 Trichloroethylene D014752 Vinyl Chloride D014810 Vitamin E C044887 beta-methylcholine C037123 cadmium sulfate C018021 cobaltous chloride C016517 indole-3-carbinol C028007 nickel monoxide C016340 o,p'-DDT C041786 palm oil C086401 pentabromodiphenyl ether C006253 pirinixic acid C045950 propiconazole C517826 tetrabrominated diphenyl ether 47 C009495 titanium dioxide C034028 vanadyl sulfate

Common Gene Haplotype Alleles


	Press "+" in the title bar above to open this section.

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 157.67 RPKM in Pituitary Total median expression: 3816.95 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


	Press "+" in the title bar above to open this section.

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-25.90	85	-0.305	Picture	PostScript	Text
3' UTR	-919.20	2367	-0.388	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on D6W5Y5


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003676 nucleic acid binding GO:0003723 RNA binding Cellular Component: GO:0005634 nucleus GO:0005730 nucleolus

Descriptions from all associated GenBank mRNAs


	AK311601 - Homo sapiens cDNA, FLJ18643. AK304185 - Homo sapiens cDNA FLJ52834 complete cds, moderately similar to Cold-inducible RNA-binding protein. AK304470 - Homo sapiens cDNA FLJ52850 complete cds, moderately similar to Cold-inducible RNA-binding protein. AK095781 - Homo sapiens cDNA FLJ38462 fis, clone FEBRA2021032, weakly similar to COLD-INDUCIBLE RNA-BINDING PROTEIN. AK128423 - Homo sapiens cDNA FLJ46566 fis, clone THYMU3040829, moderately similar to Cold-inducible RNA-binding protein. AF021336 - Homo sapiens DNA damage-inducible RNA binding protein (A18hnRNP) mRNA, complete cds. AK094781 - Homo sapiens cDNA FLJ37462 fis, clone BRAWH2011343, highly similar to COLD-INDUCIBLE RNA-BINDING PROTEIN. D78134 - Homo sapiens mRNA for CIRP, complete cds. BC000901 - Homo sapiens cold inducible RNA binding protein, mRNA (cDNA clone MGC:5232 IMAGE:2900585), complete cds. JD409166 - Sequence 390190 from Patent EP1572962. BC000403 - Homo sapiens cold inducible RNA binding protein, mRNA (cDNA clone MGC:8563 IMAGE:2822968), complete cds. HM005352 - Homo sapiens clone HTL-T-39 testicular tissue protein Li 39 mRNA, complete cds. CU674448 - Synthetic construct Homo sapiens gateway clone IMAGE:100020615 5' read CIRBP mRNA. KJ890918 - Synthetic construct Homo sapiens clone ccsbBroadEn_00312 CIRBP gene, encodes complete protein. KJ896612 - Synthetic construct Homo sapiens clone ccsbBroadEn_06006 CIRBP gene, encodes complete protein. AB528491 - Synthetic construct DNA, clone: pF1KE0611, Homo sapiens CIRBP gene for cold inducible RNA binding protein, without stop codon, in Flexi system. EU176522 - Synthetic construct Homo sapiens clone IMAGE:100011636; FLH263990.01L; RZPDo839C07245D cold inducible RNA binding protein (CIRBP) gene, encodes complete protein. EU176219 - Synthetic construct Homo sapiens clone IMAGE:100006609; FLH264005.01X; RZPDo839E10245D cold inducible RNA binding protein (CIRBP) gene, encodes complete protein. AB451348 - Homo sapiens CIRBP mRNA for cold inducible RNA binding protein, partial cds, clone: FLJ08010AAAF. BT007210 - Homo sapiens cold inducible RNA binding protein mRNA, complete cds. AB451225 - Homo sapiens CIRBP mRNA for cold inducible RNA binding protein, complete cds, clone: FLJ08010AAAN. DQ580598 - Homo sapiens piRNA piR-48710, complete sequence. DQ580105 - Homo sapiens piRNA piR-48217, complete sequence. JD019913 - Sequence 937 from Patent EP1572962. JD028917 - Sequence 9941 from Patent EP1572962. JD019716 - Sequence 740 from Patent EP1572962. JD036237 - Sequence 17261 from Patent EP1572962. JD225766 - Sequence 206790 from Patent EP1572962. DL492057 - Novel nucleic acids. DQ591424 - Homo sapiens piRNA piR-58536, complete sequence. DQ581259 - Homo sapiens piRNA piR-49371, complete sequence. JD223685 - Sequence 204709 from Patent EP1572962. JD535082 - Sequence 516106 from Patent EP1572962. JD295628 - Sequence 276652 from Patent EP1572962. AL133636 - Homo sapiens mRNA; cDNA DKFZp434H2418 (from clone DKFZp434H2418).

Other Names for This Gene


	Alternate Gene Symbols: CIRBP , D6W5Y5, D6W5Y5_HUMAN, ENST00000587896.1, ENST00000587896.2, ENST00000587896.3, ENST00000587896.4, ENST00000587896.5, hCG_21575 , NR_023312, uc326rwn.1, uc326rwn.2 UCSC ID: ENST00000587896.6_5 RefSeq Accession: NM_001300829.2 Protein: D6W5Y5

Gene Model Information


	Click here for a detailed description of the fields of the table above.

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.