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

Gene ID: 796388, updated on 2-Nov-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, Nov 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 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

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

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

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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