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    cirbpb cold inducible RNA binding protein b [ Danio rerio (zebrafish) ]

    Gene ID: 678563, updated on 27-Mar-2024

    Summary

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    Official Symbol
    cirbpbprovided by ZNC
    Official Full Name
    cold inducible RNA binding protein bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5841
    See related
    Ensembl:ENSDARG00000013351 AllianceGenome:ZFIN:ZDB-GENE-030131-5841
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    cirbp; wu:fb12c11; wu:fi20g12; zgc:136559
    Summary
    Predicted to enable RNA binding activity. Acts upstream of or within response to cold. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of spliceosomal complex. Is expressed in several structures, including gill; heart; liver; muscle; and pleuroperitoneal region. Orthologous to human CIRBP (cold inducible RNA binding protein). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See cirbpb in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (18542005..18546330, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (18517027..18521348, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene si:ch211-212d10.2 Neighboring gene si:ch211-212d10.1 Neighboring gene midnolin Neighboring gene ATP synthase F1 subunit delta

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish. Hu P, et al. Nucleic Acids Res, 2015 Oct 30. PMID 26227973, Free PMC Article
    2. Transcriptomic characterization of temperature stress responses in larval zebrafish. Long Y, et al. PLoS One, 2012. PMID 22666345, Free PMC Article
    3. Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish. McGrail M, et al. PLoS One, 2011 Apr 21. PMID 21533036, Free PMC Article
    4. A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb. Jamieson-Lucy AH, et al. Dev Biol, 2022 Apr. PMID 35065906, Free PMC Article
    5. MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae. Hung IC, et al. BMC Genomics, 2016 Nov 15. PMID 27846817, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb.
      Title: A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC136559

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to cold IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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 b; cold-inducible RNA-binding protein

    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_001040321.2 → NP_001035411.2  cold inducible RNA binding protein b isoform 1

      See identical proteins and their annotated locations for NP_001035411.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BX649404, EH436305, EH508917
      UniProtKB/TrEMBL
      A0A8M1N8U3
      Related
      ENSDARP00000096178.3, ENSDART00000105405.5
      Conserved Domains (2) summary
      COG0724
      Location:2 → 81
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:5 → 83
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001309458.1 → NP_001296387.1  cold inducible RNA binding protein b isoform 3

      See identical proteins and their annotated locations for NP_001296387.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate 3' terminal exon compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus comapred to isoform 1.
      Source sequence(s)
      BX649404
      UniProtKB/TrEMBL
      A0A8M1P6M4
      Related
      ENSDARP00000096177.3, ENSDART00000105404.5
      Conserved Domains (2) summary
      COG0724
      Location:2 → 81
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:5 → 83
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. NR_132109.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 3' structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BX649404, EH452212

    2. NR_132111.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site and an alternate 3' structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BX649404, EH447371
      Related
      ENSDART00000171277.2

    3. NR_132112.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site and an alternate terminal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BX649404, EH485709

    4. NR_132113.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses and alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BX649404, EH507728, EH508917
      Related
      ENSDART00000138915.2

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007133.7 Reference GRCz11 Primary Assembly

      Range
      18542005..18546330 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021469377.1 → XP_021325052.1  cold-inducible RNA-binding protein isoform X1

      UniProtKB/TrEMBL
      A0A8M9P4C4
      Conserved Domains (1) summary
      cl17169
      Location:5 → 83
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. XR_002456415.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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