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    ss18 SS18 subunit of BAF chromatin remodeling complex [ Danio rerio (zebrafish) ]

    Gene ID: 326668, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ss18provided by ZNC
    Official Full Name
    SS18 subunit of BAF chromatin remodeling complexprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-4867
    See related
    Ensembl:ENSDARG00000002970 AllianceGenome:ZFIN:ZDB-GENE-030131-4867
    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
    zgc:55812; wu:fe02e04
    Summary
    Predicted to enable transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in synovial sarcoma. Orthologous to human SS18 (SS18 subunit of BAF chromatin remodeling complex). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ss18 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (1348263..1364678, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (2235845..2252260, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene ATP-binding cassette, sub-family F (GCN20), member 3 Neighboring gene zinc finger protein 521 Neighboring gene uncharacterized LOC137487638 Neighboring gene desmoglein 2 like Neighboring gene si:ch73-140j24.4

    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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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity IEA
    Inferred from Electronic Annotation
    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
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein SSXT

    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_001291325.1 → NP_001278254.1  protein SSXT isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      FP101911
      UniProtKB/TrEMBL
      A0A0R4IPF8, A0A8M1P5H1
      Related
      ENSDARP00000136492.1, ENSDART00000164674.2
      Conserved Domains (1) summary
      pfam05030
      Location:16 → 73
      SSXT; SSXT protein (N-terminal region)

    2. NM_199744.2 → NP_956038.1  protein SSXT isoform 1

      See identical proteins and their annotated locations for NP_956038.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      EH553447, EH561714, FP101911
      UniProtKB/TrEMBL
      A0A8M1PDC6, Q802V1
      Related
      ENSDARP00000005954.7, ENSDART00000011919.10
      Conserved Domains (1) summary
      pfam05030
      Location:16 → 73
      SSXT; SSXT protein (N-terminal region)

    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_007113.7 Reference GRCz11 Primary Assembly

      Range
      1348263..1364678 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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