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    Sf3b1 splicing factor 3b, subunit 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84486, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sf3b1provided by RGD
    Official Full Name
    splicing factor 3b, subunit 1provided by RGD
    Primary source
    RGD:620148
    See related
    EnsemblRapid:ENSRNOG00000013516 AllianceGenome:RGD:620148
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Sap155
    Summary
    Predicted to enable chromatin binding activity; mRNA binding activity; and splicing factor binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase III and spliceosomal complex assembly. Predicted to act upstream of or within anterior/posterior pattern specification; blastocyst formation; and mRNA splicing, via spliceosome. Predicted to be located in chromatin; nuclear matrix; and nuclear speck. Predicted to be part of nucleus. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and myelodysplastic syndrome. Orthologous to human SF3B1 (splicing factor 3b subunit 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 798.0), Spleen (RPKM 680.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sf3b1 in Genome Data Viewer
    Location:
    9q31
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (63986829..64026723, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (56492403..56532300, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (61594620..61634510, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 258 B Neighboring gene ribosomal protein L11, pseudogene 6 Neighboring gene coenzyme Q10B Neighboring gene heat shock protein family D (Hsp60) member 1 Neighboring gene heat shock protein family E (Hsp10) member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Identification of anti-SF3B1 autoantibody as a diagnostic marker in patients with hepatocellular carcinoma. Hwang HM, et al. J Transl Med, 2018 Jun 28. PMID 29954402, Free PMC Article
    2. Splicing factor SF3B1 is overexpressed and implicated in the aggressiveness and survival of hepatocellular carcinoma. López-Cánovas JL, et al. Cancer Lett, 2021 Jan 1. PMID 33038489
    3. Proteomic characterization of protein phosphatase complexes of the mammalian nucleus. Tran HT, et al. Mol Cell Proteomics, 2004 Mar. PMID 14724321
    4. The SF3B1(R625H) mutation promotes prolactinoma tumor progression through aberrant splicing of DLG1. Guo J, et al. J Exp Clin Cancer Res, 2022 Jan 17. PMID 35039052, Free PMC Article
    5. Phosphorylated SAP155, the spliceosomal component, is localized to chromatin in postnatal mouse testes. Eto K, et al. Biochem Biophys Res Commun, 2010 Mar 19. PMID 20153721

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The SF3B1(R625H) mutation promotes prolactinoma tumor progression through aberrant splicing of DLG1.
      Title: The SF3B1(R625H) mutation promotes prolactinoma tumor progression through aberrant splicing of DLG1.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables splicing factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within anterior/posterior pattern specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within blastocyst formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase III ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spliceosomal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of B-WICH complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U11/U12 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U12-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U12-type spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2 snRNP ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type precatalytic spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of small nuclear ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    splicing factor 3B subunit 1
    Names
    splicing factor 3b, subunit 1, 155kD

    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_053426.1 → NP_445878.1  splicing factor 3B subunit 1

      See identical proteins and their annotated locations for NP_445878.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A8I6AP19, A6IP03, G3V7T6
      Related
      ENSRNOP00000019126.4, ENSRNOT00000019126.7
      Conserved Domains (4) summary
      smart01104
      Location:241 → 382
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
      COG5181
      Location:446 → 1304
      HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
      sd00044
      Location:850 → 874
      HEAT; HEAT repeat [structural motif]
      pfam08920
      Location:332 → 442
      SF3b1; Splicing factor 3B subunit 1

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      63986829..64026723 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017596654.2 → XP_017452143.1  splicing factor 3B subunit 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AP19
      Conserved Domains (4) summary
      smart01104
      Location:95 → 236
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
      COG5181
      Location:300 → 1158
      HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
      sd00044
      Location:704 → 728
      HEAT; HEAT repeat [structural motif]
      pfam08920
      Location:186 → 296
      SF3b1; Splicing factor 3B subunit 1

    2. XM_063267778.1 → XP_063123848.1  splicing factor 3B subunit 1 isoform X2

    3. XM_063267777.1 → XP_063123847.1  splicing factor 3B subunit 1 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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