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    si:ch211-198a12.6 si:ch211-198a12.6 [ Danio rerio (zebrafish) ]

    Gene ID: 563253, updated on 9-Dec-2024

    Summary

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    Official Symbol
    si:ch211-198a12.6provided by ZNC
    Official Full Name
    si:ch211-198a12.6provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-1683
    See related
    Ensembl:ENSDARG00000074624 AllianceGenome:ZFIN:ZDB-GENE-030131-1683
    Gene type
    protein coding
    RefSeq status
    PREDICTED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fa08f12; fb72e11; fb77h12; fc06d05; fe14e05; id:ibd2708; wu:fa08f12; wu:fb72e11; wu:fb77h12; wu:fc06d05; wu:fe14e05
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in brain; immature eye; midbrain; and otic vesicle. [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See si:ch211-198a12.6 in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (18507592..18512836)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (18376600..18381844)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene cell division cycle and apoptosis regulator 1 Neighboring gene storkhead box 1 Neighboring gene toll-like receptor 4b, duplicate a Neighboring gene toll-like receptor 4a, like

    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. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. Sreenivasan R, et al. PLoS One, 2008 Mar 12. PMID 18335061, Free PMC Article
    2. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article
    3. A gene expression screen in zebrafish embryogenesis. Kudoh T, et al. Genome Res, 2001 Dec. PMID 11731487
    4. 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
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    uncharacterized protein LOC563253

    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_001145579.1 → NP_001139051.1  uncharacterized protein LOC563253

      Status: PREDICTED

      Source sequence(s)
      BX908770
      UniProtKB/TrEMBL
      A0A8N1Z0T1, B8A688
      Related
      ENSDARP00000117362.1, ENSDART00000142622.2
      Conserved Domains (3) summary
      COG5048
      Location:247 → 523
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:282 → 302
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:323 → 347
      zf-H2C2_2; Zinc-finger double domain

    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_007124.7 Reference GRCz11 Primary Assembly

      Range
      18507592..18512836
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394876.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      133685..138934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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