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    calcoco1a calcium binding and coiled-coil domain 1a [ Danio rerio (zebrafish) ]

    Gene ID: 334971, updated on 4-Jan-2025

    Summary

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    Official Symbol
    calcoco1aprovided by ZNC
    Official Full Name
    calcium binding and coiled-coil domain 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-6911
    See related
    Ensembl:ENSDARG00000036695 AllianceGenome:ZFIN:ZDB-GENE-030131-6911
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fa11a10; calcoco1; wu:fa11a10
    Summary
    Predicted to enable transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. Orthologous to human CALCOCO1 (calcium binding and coiled-coil domain 1). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See calcoco1a in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (35981839..36003284, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (35882359..35904592, complement)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene nuclear receptor subfamily 1, group D, member 4a Neighboring gene retinoic acid receptor gamma a Neighboring gene homeobox C10a Neighboring gene homeobox C13a Neighboring gene homeobox C12a

    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. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Potok ME, et al. Cell, 2013 May 9. PMID 23663776, Free PMC Article
    2. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    3. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. 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

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    calcium-binding and coiled-coil domain-containing protein 1
    Names
    calcium binding and coiled-coil domain 1

    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_001110166.1 → NP_001103636.1  calcium-binding and coiled-coil domain-containing protein 1

      See identical proteins and their annotated locations for NP_001103636.1

      Status: PROVISIONAL

      Source sequence(s)
      BX465864
      UniProtKB/Swiss-Prot
      A2BGD5
      Related
      ENSDARP00000093924.4, ENSDART00000103150.5
      Conserved Domains (4) summary
      pfam07888
      Location:5 → 593
      CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
      pfam07956
      Location:141 → 228
      DUF1690; Protein of Unknown function (DUF1690)
      cl19107
      Location:420 → 498
      SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
      cl19219
      Location:187 → 279
      DUF342; Protein of unknown function (DUF342)

    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_007134.7 Reference GRCz11 Primary Assembly

      Range
      35981839..36003284 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009297039.4 → XP_009295314.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_009295314.1

      UniProtKB/TrEMBL
      A0A0R4IFJ0, A0A8M3AVM8
      Related
      ENSDARP00000131607.1, ENSDART00000164699.3
      Conserved Domains (5) summary
      pfam07888
      Location:5 → 604
      CALCOCO1; Calcium binding and coiled-coil domain (CALCOCO1) like
      pfam07956
      Location:141 → 228
      DUF1690; Protein of Unknown function (DUF1690)
      cl19107
      Location:420 → 509
      SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
      cl19219
      Location:187 → 279
      DUF342; Protein of unknown function (DUF342)
      cl19849
      Location:473 → 518
      DUF881; Bacterial protein of unknown function (DUF881)

    2. XM_068216688.1 → XP_068072789.1  calcium-binding and coiled-coil domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0R4IFJ0, A0A8M3AVM8
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2BGD5.1 GenPept UniProtKB/Swiss-Prot:A2BGD5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.