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

    Gene ID: 1153, updated on 10-Jun-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CIRBP in Genome Data Viewer
    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_000019.10Genomic 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

    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 Functions

    What'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

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001280.3NP_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:685
      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_001300815.2NP_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:685
      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_001300829.2NP_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/TrEMBL
      D6W5Y5
      Related
      ENSP00000466025.1, ENST00000587896.6
      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_023312.3 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_2023_10

    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_017026237.2XP_016881726.1  cold-inducible RNA-binding protein isoform X3

      UniProtKB/TrEMBL
      K7EMY9, K7EPM4
      Related
      ENSP00000468645.1, ENST00000586773.5
      Conserved Domains (1) summary
      cd12449
      Location:685
      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_011527668.1XP_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
      B3KT17, B4E2X2, Q14011
      UniProtKB/TrEMBL
      K7EMY9, Q53XX5
      Related
      ENSP00000466110.1, ENST00000585630.5
      Conserved Domains (1) summary
      cd12449
      Location:685
      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_054319716.1XP_054175691.1  cold-inducible RNA-binding protein isoform X3

      UniProtKB/TrEMBL
      K7EMY9, K7EPM4
    2. XM_054319714.1XP_054175689.1  cold-inducible RNA-binding protein isoform X1

      UniProtKB/TrEMBL
      K7EQR7
    3. XM_054319715.1XP_054175690.1  cold-inducible RNA-binding protein isoform X2

      UniProtKB/Swiss-Prot
      B3KT17, B4E2X2, Q14011
      UniProtKB/TrEMBL
      K7EMY9, Q53XX5

    RNA

    1. XR_008485080.1 RNA Sequence

    2. XR_008485079.1 RNA Sequence