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    scaf4a SR-related CTD-associated factor 4a [ Danio rerio (zebrafish) ]

    Gene ID: 567501, updated on 16-Apr-2024

    Summary

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    Official Symbol
    scaf4aprovided by ZNC
    Official Full Name
    SR-related CTD-associated factor 4aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-9003
    See related
    Ensembl:ENSDARG00000077093 AllianceGenome:ZFIN:ZDB-GENE-030131-9003
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fa96d07; wu:fa96d07; si:dkey-50p8.3
    Summary
    Predicted to enable RNA binding activity. Orthologous to human SCAF4 (SR-related CTD associated factor 4). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See scaf4a in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (25700812..25716871, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (25739082..25755160, complement)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene TIAM Rac1 associated GEF 1a Neighboring gene superoxide dismutase 1, soluble Neighboring gene UDP glucuronosyltransferase 5 family, polypeptide D1 Neighboring gene periostin, osteoblast specific factor a

    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. The spatial-temporal expression and functional divergence of bach homologs in zebrafish Danio rerio. Luo Q, et al. J Fish Biol, 2016 Apr. PMID 26992035
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, 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
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
      Title: SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    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 RNA polymerase II C-terminal domain phosphoserine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled 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
    splicing factor, arginine/serine-rich 15

    NCBI Reference Sequences (RefSeq)

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    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_007121.7 Reference GRCz11 Primary Assembly

      Range
      25700812..25716871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_690795.8 → XP_695887.5  splicing factor, arginine/serine-rich 15

      UniProtKB/TrEMBL
      A0A8N7TBP0, E7F4U8
      Related
      ENSDARP00000107896.2, ENSDART00000125665.4
      Conserved Domains (4) summary
      COG0724
      Location:454 → 519
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd03562
      Location:4 → 125
      CID; CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA ...
      pfam07271
      Location:583 → 748
      Cytadhesin_P30; Cytadhesin P30/P32
      cl17169
      Location:454 → 534
      RRM_SF; RNA recognition motif (RRM) superfamily
    Nucleotide Protein
    Heading Accession and Version

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