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    chico chico [ Danio rerio (zebrafish) ]

    Gene ID: 30067, updated on 27-Mar-2024

    Summary

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    Official Symbol
    chicoprovided by ZNC
    Official Full Name
    chicoprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000210-28
    See related
    Ensembl:ENSDARG00000019588 AllianceGenome:ZFIN:ZDB-GENE-000210-28
    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
    Summary
    Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human TLE5 (TLE family member 5, transcriptional modulator). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See chico in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (52406565..52455565, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (52812627..52862065, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene phospholipid phosphatase 2a Neighboring gene TLE family member 2, transcriptional corepressor c Neighboring gene guanine nucleotide binding protein (G protein), alpha 11b (Gq class) Neighboring gene uncharacterized LOC101885297

    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    chico

    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_001312685.1 → NP_001299614.1  chico

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses alternate splice sites in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      CABZ01042148, CU570695, CU571311
      UniProtKB/TrEMBL
      A0A0R4IZ81, A0A8N7XJ84, F6NKM6, Q9PTS6
      Related
      ENSDARP00000007256.6, ENSDART00000002241.7
      Conserved Domains (1) summary
      pfam03920
      Location:2 → 132
      TLE_N; Groucho/TLE N-terminal Q-rich domain

    2. NM_130911.2 → NP_570986.1  chico

      See identical proteins and their annotated locations for NP_570986.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variant 1 and 2 encode the same protein.
      Source sequence(s)
      CABZ01042148, CU570695, CU571311
      UniProtKB/TrEMBL
      A0A0R4IZ81, A0A8N7XJ84, F6NKM6, Q9PTS6
      Related
      ENSDARP00000141688.1, ENSDART00000160768.2
      Conserved Domains (1) summary
      pfam03920
      Location:2 → 132
      TLE_N; Groucho/TLE N-terminal Q-rich domain

    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_007113.7 Reference GRCz11 Primary Assembly

      Range
      52406565..52455565 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009298917.3 → XP_009297192.1  chico isoform X1

      UniProtKB/TrEMBL
      A0A8M3AQ33
      Conserved Domains (1) summary
      pfam03920
      Location:2 → 131
      TLE_N; Groucho/TLE N-terminal Q-rich domain
    Nucleotide Protein Strain
    Heading Accession and Version

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