SF3B1 splicing factor 3b subunit 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SF3B1provided by HGNC
Official Full Name: splicing factor 3b subunit 1provided by HGNC
Primary source: HGNC:HGNC:10768
See related: Ensembl:ENSG00000115524 MIM:605590; AllianceGenome:HGNC:10768
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: MDS; PRP10; Hsh155; PRPF10; SAP155; SF3b155
Summary: This gene encodes subunit 1 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. The carboxy-terminal two-thirds of subunit 1 have 22 non-identical, tandem HEAT repeats that form rod-like, helical structures. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in lymph node (RPKM 87.0), bone marrow (RPKM 86.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q33.1

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (197389784..197435093, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (197873439..197918732, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (198254508..198299817, complement)

Chromosome 2 - NC_000002.12 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?

The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.
Title: The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.
The splicing factor SF3B1 confers ferroptosis resistance and promotes lung adenocarcinoma progression via upregulation of SLC7A11.
Title: The splicing factor SF3B1 confers ferroptosis resistance and promotes lung adenocarcinoma progression via upregulation of SLC7A11.
GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies.
Title: GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies.
Mutations in the splicing factor SF3B1 are linked to frequent emergence of HLA-DR[low/neg] monocytes in lower-risk myelodysplastic neoplasms.
Title: Mutations in the splicing factor SF3B1 are linked to frequent emergence of HLA-DR(low/neg) monocytes in lower-risk myelodysplastic neoplasms.
Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.
Title: Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.
SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia.
Title: SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia.
Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.
Title: Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.
IMMUNOPHENOTYPE OF LEUKEMIC CELLS IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS WITH NOTCH1 AND SF3B1 GENE MUTATIONS.
Title: IMMUNOPHENOTYPE OF LEUKEMIC CELLS IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS WITH NOTCH1 AND SF3B1 GENE MUTATIONS.
Expression of circular RNAs in myelodysplastic neoplasms and their association with mutations in the splicing factor gene SF3B1.
Title: Expression of circular RNAs in myelodysplastic neoplasms and their association with mutations in the splicing factor gene SF3B1.
Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma.
Title: Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma.

Submit: New GeneRIF Correction See all GeneRIFs (222)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Myelodysplastic syndrome MedGen: C3463824 OMIM: 614286 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. 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 1 (SF3B1) 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 155kDa subunit 1 of splicing factor 3b (SF3B1; SAP155), 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 155kDa subunit 1 of splicing factor 3b (SF3B1; SAP155), 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 155kDa subunit 1 of splicing factor 3b (SF3B1; SAP155), 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 155kDa subunit 1 of splicing factor 3b (SF3B1; SAP155), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_15343-15344:1013437555:1 (e-PCR)
- UniSTS:267820

D2S1533E (e-PCR)
- UniSTS:20300

G54156 (e-PCR)
- UniSTS:109393

EST23H7 (e-PCR)
- UniSTS:263259

RH66152 (e-PCR)
- UniSTS:3420

SF3B1-1 (e-PCR)
- UniSTS:513652

RH118649 (e-PCR)
- UniSTS:138142

MARC_11487-11488:1000830916:1 (e-PCR)
- UniSTS:267202

A006O45 (e-PCR)
- UniSTS:57033

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables splicing factor binding	IDA Inferred from Direct Assay more info	PubMed
enables splicing factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	IC Inferred by Curator more info	PubMed
involved_in RNA splicing, via transesterification reactions	NAS Non-traceable Author Statement more info	PubMed
involved_in U2-type prespliceosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
acts_upstream_of_or_within mRNA splicing, via spliceosome	IDA Inferred from Direct Assay 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
involved_in positive regulation of transcription by RNA polymerase I	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase III	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of B-WICH complex	IDA Inferred from Direct Assay more info	PubMed
part_of U11/U12 snRNP	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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 prespliceosome	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 nucleolus	NAS Non-traceable Author Statement more info	PubMed
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 spliceosomal complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: splicing factor 3B subunit 1

Names: pre-mRNA processing 10; pre-mRNA splicing factor SF3b, 155 kDa subunit; spliceosome-associated protein 155; splicing factor 3b, subunit 1, 155kDa

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.

Genomic

NG_032903.2 RefSeqGene

Range

4955..48074

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_624

mRNA and Protein(s)

NM_001005526.2 → NP_001005526.1 splicing factor 3B subunit 1 isoform 2

See identical proteins and their annotated locations for NP_001005526.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes a shorter isoform (2) which has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AK294851, BC046140, HY054349

Consensus CDS

CCDS46479.1

UniProtKB/TrEMBL

A8K355

Related

ENSP00000402997.2, ENST00000414963.2
NM_001308824.1 → NP_001295753.1 splicing factor 3B subunit 1 isoform 3

See identical proteins and their annotated locations for NP_001295753.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK294851, BC046140, HY054349

Consensus CDS

CCDS82550.1

UniProtKB/TrEMBL

A8K355, B4DGZ4

Related

ENSP00000419896.1, ENST00000487698.5
NM_012433.4 → NP_036565.2 splicing factor 3B subunit 1 isoform 1

See identical proteins and their annotated locations for NP_036565.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC010746, AF054284, AF070540, AK294851, BC039020, BE168209

Consensus CDS

CCDS33356.1

UniProtKB/Swiss-Prot

E9PCH3, O75533

Related

ENSP00000335321.6, ENST00000335508.11

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_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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

197389784..197435093 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047443838.1 → XP_047299794.1 splicing factor 3B subunit 1 isoform X1

Related

ENST00000470268.2
XM_047443839.1 → XP_047299795.1 splicing factor 3B subunit 1 isoform X1
XM_047443840.1 → XP_047299796.1 splicing factor 3B subunit 1 isoform X2
XM_047443841.1 → XP_047299797.1 splicing factor 3B subunit 1 isoform X3

UniProtKB/TrEMBL

A8K355

Related

ENSP00000428820.1, ENST00000409915.8

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

197873439..197918732 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341208.1 → XP_054197183.1 splicing factor 3B subunit 1 isoform X1
XM_054341209.1 → XP_054197184.1 splicing factor 3B subunit 1 isoform X1
XM_054341210.1 → XP_054197185.1 splicing factor 3B subunit 1 isoform X2
XM_054341211.1 → XP_054197186.1 splicing factor 3B subunit 1 isoform X3

UniProtKB/TrEMBL

A8K355