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    scaf4b SR-related CTD-associated factor 4b [ Danio rerio (zebrafish) ]

    Gene ID: 552961, updated on 9-Dec-2024

    Summary

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    Official Symbol
    scaf4bprovided by ZNC
    Official Full Name
    SR-related CTD-associated factor 4bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050506-42
    See related
    Ensembl:ENSDARG00000018854 AllianceGenome:ZFIN:ZDB-GENE-050506-42
    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
    im:6900467; si:ch211-245g11.2
    Summary
    Predicted to enable RNA binding activity and RNA polymerase II C-terminal domain phosphoserine binding activity. Predicted to be involved in negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled. Predicted to be active in nucleus. Orthologous to human SCAF4 (SR-related CTD associated factor 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See scaf4b in Genome Data Viewer
    Location:
    chromosome: 15
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (42285637..42347217)
    105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (42329302..42390865)

    Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene phenylalanyl-tRNA synthetase subunit beta Neighboring gene TIAM Rac1 associated GEF 1b Neighboring gene claudin 8.2 Neighboring gene claudin 8.3

    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. SCAF4 variants associated with focal epilepsy accompanied by multisystem disorders. Lin H, et al. Seizure, 2024 Mar. PMID 37394306
    2. A versatile gene trap to visualize and interrogate the function of the vertebrate proteome. Trinh le A, et al. Genes Dev, 2011 Nov 1. PMID 22056673, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    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

    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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    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 molecular_function ND
    No biological Data available
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    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
    SR-related and CTD-associated factor 4b
    Names
    splicing factor, arginine/serine-rich 15

    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_001386228.1 → NP_001373157.1  SR-related and CTD-associated factor 4b isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BX322538
      UniProtKB/TrEMBL
      A0A8N7UV04, R4GE22
      Related
      ENSDARP00000126734.1, ENSDART00000152731.2
      Conserved Domains (3) summary
      PHA03247
      Location:708 → 902
      PHA03247; large tegument protein UL36; Provisional
      cd17005
      Location:7 → 137
      CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
      cl17169
      Location:502 → 582
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_001386229.1 → NP_001373158.1  SR-related and CTD-associated factor 4b isoform 2

      Status: VALIDATED

      Source sequence(s)
      BX322538
      UniProtKB/TrEMBL
      A0A8M6YV44
      Related
      ENSDARP00000090006.3, ENSDART00000099234.6
      Conserved Domains (4) summary
      PHA03247
      Location:186 → 345
      PHA03247; large tegument protein UL36; Provisional
      COG0724
      Location:502 → 692
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd17005
      Location:7 → 137
      CID_SFRS15_SCAF4; CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15
      cl17169
      Location:502 → 582
      RRM_SF; RNA recognition motif (RRM) superfamily

    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_007126.7 Reference GRCz11 Primary Assembly

      Range
      42285637..42347217
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068213554.1 → XP_068069655.1  SR-related and CTD-associated factor 4b isoform X1

    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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