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    sf3a1 splicing factor 3a, subunit 1 [ Danio rerio (zebrafish) ]

    Gene ID: 796388, updated on 9-Dec-2024

    Summary

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    Official Symbol
    sf3a1provided by ZNC
    Official Full Name
    splicing factor 3a, subunit 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030616-156
    See related
    Ensembl:ENSDARG00000041887 AllianceGenome:ZFIN:ZDB-GENE-030616-156
    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
    zgc:65786; wu:fc38e01; wu:fc50a11; wu:fj37c05; si:dz150f13.2
    Summary
    Predicted to enable RNA binding activity. Predicted to act upstream of or within mRNA cis splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of U2 snRNP; U2-type prespliceosome; and catalytic step 2 spliceosome. Orthologous to human SF3A1 (splicing factor 3a subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See sf3a1 in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (36554807..36570235)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (36520435..36537802)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137496284 Neighboring gene coiled-coil domain containing 157 Neighboring gene polymerase (DNA directed), delta 2, regulatory subunit Neighboring gene 5S ribosomal RNA

    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 zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    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. 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
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. 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

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC65786, MGC77239

    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
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA cis splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of U2 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    splicing factor 3A subunit 1
    Names
    splicing factor 3a, subunit 1, 120kDa

    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_200094.1 → NP_956388.1  splicing factor 3A subunit 1

      See identical proteins and their annotated locations for NP_956388.1

      Status: PROVISIONAL

      Source sequence(s)
      BC056521
      UniProtKB/TrEMBL
      B7ZV97, Q90X41
      Related
      ENSDARP00000061377.2, ENSDART00000061378.3
      Conserved Domains (4) summary
      cd01800
      Location:705 → 780
      SF3a120_C; Ubiquitin-like domain of Mammalian splicing factor SF3a_120
      smart00648
      Location:41 → 94
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam01805
      Location:151 → 201
      Surp; Surp module
      pfam12230
      Location:218 → 459
      PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein

    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_007119.7 Reference GRCz11 Primary Assembly

      Range
      36554807..36570235
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005167228.5 → XP_005167285.1  splicing factor 3A subunit 1 isoform X1

      See identical proteins and their annotated locations for XP_005167285.1

      UniProtKB/TrEMBL
      B7ZV97, Q90X41
      Related
      ENSDARP00000108576.2, ENSDART00000126687.4
      Conserved Domains (4) summary
      cd01800
      Location:705 → 780
      SF3a120_C; Ubiquitin-like domain of Mammalian splicing factor SF3a_120
      smart00648
      Location:41 → 94
      SWAP; Suppressor-of-White-APricot splicing regulator
      pfam01805
      Location:151 → 201
      Surp; Surp module
      pfam12230
      Location:218 → 459
      PRP21_like_P; Pre-mRNA splicing factor PRP21 like protein

    2. XM_068223034.1 → XP_068079135.1  splicing factor 3A subunit 1 isoform X1

      UniProtKB/TrEMBL
      B7ZV97, Q90X41

    3. XM_068223035.1 → XP_068079136.1  splicing factor 3A subunit 1 isoform X1

      UniProtKB/TrEMBL
      B7ZV97, Q90X41

    4. XM_068223036.1 → XP_068079137.1  splicing factor 3A subunit 1 isoform X1

      UniProtKB/TrEMBL
      B7ZV97, Q90X41
    Nucleotide Protein Strain
    Heading Accession and Version

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