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

Gene ID: 10992, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:10769
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
CFM; HFM; 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
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Genomic context

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Location:
11q13.1
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66052364..66069308)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66046496..66063445)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65819835..65836779)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65790121-65790622 Neighboring gene cation channel sperm associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65818833-65819384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5028 Neighboring gene galactose-3-O-sulfotransferase 3 Neighboring gene small nucleolar RNA, C/D box 13F Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3575 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65838483-65838687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5031 Neighboring gene phosphofurin acidic cluster sorting protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65866985-65867894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65867895-65868802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65874431-65875274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5034 Neighboring gene Sharpr-MPRA regulatory region 6316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65894813-65895472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3580 Neighboring gene small nucleolar RNA U13 Neighboring gene uncharacterized LOC105369354

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Haploinsufficiency of SF3B2 causes craniofacial microsomia. Timberlake AT, et al. Nat Commun, 2021 Aug 3. PMID 34344887, Free PMC Article
  2. G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression. Matsumoto K, et al. Genes Cells, 2021 Feb. PMID 33290632, Free PMC Article
  3. Multiple roles of the splicing complex SF3B in DNA end resection and homologous recombination. Prados-Carvajal R, et al. DNA Repair (Amst), 2018 Jun-Jul. PMID 29705135
  4. Hemifacial microsomia: progress in understanding the genetic basis of a complex malformation syndrome. Kelberman D, et al. Hum Genet, 2001 Dec. PMID 11810276
  5. Herpes simplex virus IE63 (ICP27) protein interacts with spliceosome-associated protein 145 and inhibits splicing prior to the first catalytic step. Bryant HE, et al. J Virol, 2001 May. PMID 11287586, Free PMC Article

See all (232) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Haploinsufficiency of SF3B2 causes craniofacial microsomia.
    Title: Haploinsufficiency of SF3B2 causes craniofacial microsomia.
  2. G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression.
    Title: G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression.
  3. SF3B2 is a critical determinant of AR-V7 expression and is correlated with aggressive cancer phenotypes. Pladienolide B, an inhibitor of a splicing modulator of the SF3b complex, suppressed the growth of tumors addicted to high SF3B2 expression. SF3B2 is a critical determinant of RNA splicing and gene expression patterns and controls the expression of key genes associated with CRPC progression, such as AR-V7.
    Title: SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression.
  4. Splicing complex SF3B depletion impairs DNA end resection and hampers homologous recombination repair. SF3B controls CtIP function at, as least, two levels: by affecting CtIP mRNA levels and controlling CtIP recruitment to DNA breaks, in a way that requires ATM-mediated phosphorylation of SF3B2 at serine 289.
    Title: Multiple roles of the splicing complex SF3B in DNA end resection and homologous recombination.
  5. a docking model based on NOESY measurements suggests that residues 607-616 of the SF3b145 fragment adopt a helical structure that binds to RRM1 predominantly via alpha1, consequently exhibiting a helix-helix interaction in almost antiparallel.
    Title: Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.
  6. High SF3B2 expression is associated with hepatocellular carcinoma.
    Title: Meta-analysis of gene expression profiles indicates genes in spliceosome pathway are up-regulated in hepatocellular carcinoma (HCC).
  7. Although amino acid substitutions of residues surrounding Arg-508 had no great effect on PRMT9 recognition of SF3B2, moving the arginine residue within this sequence abolished methylation.
    Title: Unique Features of Human Protein Arginine Methyltransferase 9 (PRMT9) and Its Substrate RNA Splicing Factor SF3B2.
  8. Inhibiting the induction of two proteins involved in two of the most significantly upregulated cellular processes, ribosome biogenesis (eIF6) and hnRNA splicing (SF3B2/SF3B4), showed that human T cells can enter the cell cycle without growing in size.
    Title: Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry.
  9. Data show that Vpr induces checkpoint activation and G(2) 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).
    Title: Human immunodeficiency virus type 1 Vpr induces G2 checkpoint activation by interacting with the splicing factor SAP145.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Craniofacial microsomia 1
MedGen: CN376809 OMIM: 164210 GeneReviews: Not available
not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 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 GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in U2-type prespliceosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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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)

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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_006842.3 → NP_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
    A8K485, B4DT19, Q13435, Q7L4T5, Q7Z627, Q969K1, Q96CM6, Q9BWD2
    UniProtKB/TrEMBL
    E9PPJ0
    Related
    ENSP00000318861.6, ENST00000322535.11
    Conserved Domains (3) summary
    COG5182
    Location:442 → 706
    CUS1; Splicing factor 3b, subunit 2 [RNA processing and modification]
    pfam02037
    Location:24 → 57
    SAP; SAP domain
    pfam04037
    Location:471 → 596
    DUF382; Domain of unknown function (DUF382)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66052364..66069308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005273726.5 → XP_005273783.1  splicing factor 3B subunit 2 isoform X2

    See identical proteins and their annotated locations for XP_005273783.1

    UniProtKB/TrEMBL
    E9PPJ0
    Conserved Domains (3) summary
    COG5182
    Location:441 → 705
    CUS1; Splicing factor 3b, subunit 2 [RNA processing and modification]
    pfam02037
    Location:30 → 57
    SAP; SAP domain
    pfam04037
    Location:470 → 595
    DUF382; Domain of unknown function (DUF382)

  2. XM_011544740.4 → XP_011543042.1  splicing factor 3B subunit 2 isoform X1

    See identical proteins and their annotated locations for XP_011543042.1

    UniProtKB/TrEMBL
    E9PPJ0
    Related
    ENSP00000432655.1, ENST00000528302.5
    Conserved Domains (3) summary
    COG5182
    Location:441 → 705
    CUS1; Splicing factor 3b, subunit 2 [RNA processing and modification]
    pfam02037
    Location:30 → 57
    SAP; SAP domain
    pfam04037
    Location:470 → 595
    DUF382; Domain of unknown function (DUF382)

  3. XM_017017144.3 → XP_016872633.1  splicing factor 3B subunit 2 isoform X3

    UniProtKB/TrEMBL
    E9PPJ0
    Conserved Domains (3) summary
    COG5182
    Location:440 → 704
    CUS1; Splicing factor 3b, subunit 2 [RNA processing and modification]
    pfam02037
    Location:30 → 57
    SAP; SAP domain
    pfam04037
    Location:469 → 594
    DUF382; Domain of unknown function (DUF382)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66046496..66063445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367533.1 → XP_054223508.1  splicing factor 3B subunit 2 isoform X2

  2. XM_054367532.1 → XP_054223507.1  splicing factor 3B subunit 2 isoform X1

  3. XM_054367534.1 → XP_054223509.1  splicing factor 3B subunit 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13435.2 GenPept UniProtKB/Swiss-Prot:Q13435

Gene LinkOut

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