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

Gene ID: 678563, updated on 9-Dec-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 several human genes including CIRBP (cold inducible RNA binding protein). [provided by Alliance of Genome Resources, Dec 2024]
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
RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (18542005..18546326, 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 cartilage intermediate layer protein 2 Neighboring gene uncharacterized LOC137488919 Neighboring gene midnolin

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 IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
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
  

General protein information

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Preferred Names
cold inducible RNA binding protein b

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, A0A8M9P4C4
    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, A0A8M9P4C4
    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

  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: GCF_000002035.6-RS_2024_08

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..18546326 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_002456415.2 RNA Sequence

    Related
    ENSDART00000171277.2
Nucleotide Protein Strain
Heading Accession and Version

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