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

Gene ID: 84486, updated on 13-Apr-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
Ensembl: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 spliceosomal complex assembly. Predicted to act upstream of or within anterior/posterior pattern specification; blastocyst formation; and mRNA splicing, via spliceosome. Located in 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, Apr 2022]
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
  
part_of 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, ENSRNOT00000019126.6
    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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