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

Gene ID: 23451, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See SF3B1 in Genome Data Viewer
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_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12212 Neighboring gene ANKRD44 divergent transcript Neighboring gene nucleophosmin 1 pseudogene 46 Neighboring gene small nucleolar RNA SNORA4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:198299380-198300579 Neighboring gene RNA, U6 small nuclear 1029, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16935 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:198317938-198318554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16938 Neighboring gene uncharacterized LOC124907951 Neighboring gene coenzyme Q10B

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 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. Functional genomics identifies a requirement of pre-mRNA splicing factors for sister chromatid cohesion. Sundaramoorthy S, et al. EMBO J, 2014 Nov 18. PMID 25257310, Free PMC Article
  2. SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts. Malcovati L, et al. Blood, 2015 Jul 9. PMID 25957392, Free PMC Article
  3. SF3B1 deficiency impairs human erythropoiesis via activation of p53 pathway: implications for understanding of ineffective erythropoiesis in MDS. Huang Y, et al. J Hematol Oncol, 2018 Feb 12. PMID 29433555, Free PMC Article
  4. SF3B1 association with chromatin determines splicing outcomes. Kfir N, et al. Cell Rep, 2015 Apr 28. PMID 25892229
  5. Cancer-Associated SF3B1 Mutations Confer a BRCA-Like Cellular Phenotype and Synthetic Lethality to PARP Inhibitors. Lappin KM, et al. Cancer Res, 2022 Mar 1. PMID 35027467, Free PMC Article

See all (495) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies.
    Title: GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. [Clinical and laboratory features of SF3B1-mutated myeloproliferative neoplasms].
    Title: [Clinical and laboratory features of SF3B1-mutated myeloproliferative neoplasms].
Submit: New GeneRIF Correction See all GeneRIFs (221)

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
Myelodysplastic syndrome
MedGen: C3463824 OMIM: 614286 GeneReviews: Not available
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EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
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 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

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 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

  1. NG_032903.2 RefSeqGene

    Range
    4955..48074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_624

mRNA and Protein(s)

  1. 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

  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

  3. 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

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    197389784..197435093 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Related
    ENST00000470268.2

  2. XM_047443839.1 → XP_047299795.1  splicing factor 3B subunit 1 isoform X1

  3. XM_047443840.1 → XP_047299796.1  splicing factor 3B subunit 1 isoform X2

  4. XM_047443841.1 → XP_047299797.1  splicing factor 3B subunit 1 isoform X3

    Related
    ENSP00000428820.1, ENST00000409915.8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    197873439..197918732 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341208.1 → XP_054197183.1  splicing factor 3B subunit 1 isoform X1

  2. XM_054341209.1 → XP_054197184.1  splicing factor 3B subunit 1 isoform X1

  3. XM_054341210.1 → XP_054197185.1  splicing factor 3B subunit 1 isoform X2

  4. XM_054341211.1 → XP_054197186.1  splicing factor 3B subunit 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75533.3 GenPept UniProtKB/Swiss-Prot:O75533

Gene LinkOut

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