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

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; 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: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (66052364..66069308)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (66046496..66063445)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (65819835..65836779)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Haploinsufficiency of SF3B2 causes craniofacial microsomia.
Title: Haploinsufficiency of SF3B2 causes craniofacial microsomia.
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.
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.
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.
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.
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).
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.
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.
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.

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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: C3495417 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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

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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

MARC_24069-24070:1030027541:1 (e-PCR)
- UniSTS:268840

PMC156606P1 (e-PCR)
- UniSTS:271408

SHGC-67307 (e-PCR)
- UniSTS:89991

D11S3316 (e-PCR)
- UniSTS:152558

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

66052364..66069308

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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

NC_060935.1 Alternate T2T-CHM13v2.0

Range

66046496..66063445

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

E9PPJ0
XM_054367532.1 → XP_054223507.1 splicing factor 3B subunit 2 isoform X1

UniProtKB/TrEMBL

E9PPJ0
XM_054367534.1 → XP_054223509.1 splicing factor 3B subunit 2 isoform X3

UniProtKB/TrEMBL

E9PPJ0