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SF3B2 splicing factor 3b subunit 2 [ Homo sapiens (human) ]

Gene ID: 10992, updated on 10-Oct-2019

Summary

Official Symbol
SF3B2provided by HGNC
Official Full Name
splicing factor 3b subunit 2provided by HGNC
Primary source
HGNC:HGNC:10769
See related
Ensembl:ENSG00000087365 MIM:605591
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Cus1; SF3b1; SAP145; SF3B145; SF3b150
Summary
This gene encodes subunit 2 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. Splicing factor 3b is also a component of the minor U12-type spliceosome. Subunit 2 associates with pre-mRNA upstream of the branch site at the anchoring site. Subunit 2 also interacts directly with subunit 4 of the splicing factor 3b complex. Subunit 2 is a highly hydrophilic protein with a proline-rich N-terminus and a glutamate-rich stretch in the C-terminus. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 65.1), ovary (RPKM 47.8) and 25 other tissues See more
Orthologs

Genomic context

See SF3B2 in Genome Data Viewer
Location:
11q13.1
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (66052361..66069308)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65819264..65836382)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene cation channel sperm associated 1 Neighboring gene galactose-3-O-sulfotransferase 3 Neighboring gene small nucleolar RNA, C/D box 13F Neighboring gene phosphofurin acidic cluster sorting protein 1 Neighboring gene uncharacterized LOC105369354 Neighboring gene uncharacterized LOC105369352 Neighboring gene kinesin light chain 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of splicing factor 3b, subunit 2 (SF3B2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify splicing factor 3b subunit 2 (SF3B2; 145kDa), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify splicing factor 3b subunit 2 (SF3B2; 145kDa), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify splicing factor 3b subunit 2 (SF3B2; 145kDa), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify splicing factor 3b subunit 2 (SF3B2; 145kDa), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Vpr vpr Interaction of HIV-1 Vpr with SAP145 inhibits SAP145-SAP49 complex formation PubMed
vpr HIV-1 Vpr induces checkpoint activation and G2 arrest by binding to the CUS1 domain of SAP145 and interfering with the functions of the SAP145 and SAP49 proteins, two subunits of the multimeric splicing factor 3b (SF3b) PubMed
vpr HIV-1 Vpr interacts with and co-localizes with SAP145; this interaction is mediated through the C-terminal domain (residues 49-96) of Vpr PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human splicing factor 3b, subunit 2, 145kDa (SF3B2) at amino acid residues 668-669 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U2-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U2-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U2-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U2-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
mRNA processing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
splicing factor 3B subunit 2
Names
SAP 145
pre-mRNA splicing factor SF3b 145 kDa subunit
spliceosome associated protein 145
splicing factor 3b, subunit 2, 145kD
splicing factor 3b, subunit 2, 145kDa

NCBI Reference Sequences (RefSeq)

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_006842.3NP_006833.2  splicing factor 3B subunit 2

    See identical proteins and their annotated locations for NP_006833.2

    Status: REVIEWED

    Source sequence(s)
    AP006287, BC014125, BC053577, BE677116, BF311442
    Consensus CDS
    CCDS31612.1
    UniProtKB/Swiss-Prot
    Q13435
    Related
    ENSP00000318861.6, ENST00000322535.11
    Conserved Domains (3) summary
    smart00513
    Location:2458
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    COG5182
    Location:442706
    CUS1; Splicing factor 3b, subunit 2 [RNA processing and modification]
    pfam04037
    Location:471596
    DUF382; Domain of unknown function (DUF382)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    66052361..66069308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005273726.4XP_005273783.1  splicing factor 3B subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_005273783.1

    Conserved Domains (3) summary
    smart00581
    Location:600658
    PSP; proline-rich domain in spliceosome associated proteins
    pfam02037
    Location:2457
    SAP; SAP domain
    pfam04037
    Location:470595
    DUF382; Domain of unknown function (DUF382)
  2. XM_011544740.3XP_011543042.1  splicing factor 3B subunit 2 isoform X2

    See identical proteins and their annotated locations for XP_011543042.1

    Conserved Domains (3) summary
    smart00581
    Location:600658
    PSP; proline-rich domain in spliceosome associated proteins
    pfam02037
    Location:2457
    SAP; SAP domain
    pfam04037
    Location:470595
    DUF382; Domain of unknown function (DUF382)
  3. XM_017017144.2XP_016872633.1  splicing factor 3B subunit 2 isoform X3

    Conserved Domains (3) summary
    smart00581
    Location:599657
    PSP; proline-rich domain in spliceosome associated proteins
    pfam02037
    Location:2457
    SAP; SAP domain
    pfam04037
    Location:469594
    DUF382; Domain of unknown function (DUF382)
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