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

Gene ID: 23451, updated on 4-Nov-2018

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; Vega:OTTHUMG00000154447
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

Genomic context

See SF3B1 in Genome Data Viewer
Location:
2q33.1
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (197391974..197435093, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (198256698..198299815, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373824 Neighboring gene nucleophosmin 1 pseudogene 46 Neighboring gene RNA, U6 small nuclear 1029, pseudogene Neighboring gene coenzyme Q10B

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog

HIV-1 interactions

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 BioSystems

  • B-WICH complex positively regulates rRNA expression, organism-specific biosystem (from REACTOME)
    B-WICH complex positively regulates rRNA expression, organism-specific biosystemThe B-WICH complex is a large 3 Mdalton complex containing SMARCA5 (SNF2H), BAZ1B (WSTF), ERCC6 (CSB), MYO1C (Nuclear myosin 1c) (Cavellan et al. 2006, Percipalle et al. 2006, Vintermist et al. 2001,...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • 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...
  • Positive epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
    Positive epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in Percipalle and Farrants 2006, McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2...
  • 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 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing, via transesterification reactions NAS
Non-traceable Author Statement
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 NAS
Non-traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
positive regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
spliceosomal complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
U11/U12 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
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 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
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 NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

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)

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_001005526.2NP_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
    B4DGZ4
    Related
    ENSP00000402997.2, OTTHUMP00000225002, ENST00000414963.2, OTTHUMT00000375708
  2. NM_001308824.1NP_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
    B4DGZ4
    Related
    ENSP00000419896.1, OTTHUMP00000205702, ENST00000487698.5, OTTHUMT00000335248
  3. NM_012433.3NP_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)
    AF054284, AF070540, AK294851, BC039020, BE168209, HY054349
    Consensus CDS
    CCDS33356.1
    UniProtKB/Swiss-Prot
    O75533
    UniProtKB/TrEMBL
    B4DGZ4
    Related
    ENSP00000335321.5, OTTHUMP00000205700, ENST00000335508.10, OTTHUMT00000335245
    Conserved Domains (4) summary
    smart01104
    Location:241382
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    COG5181
    Location:4461304
    HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
    sd00044
    Location:850874
    HEAT; HEAT repeat [structural motif]
    pfam08920
    Location:332443
    SF3b1; Splicing factor 3B subunit 1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    197391974..197435093 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001738680.2 RNA Sequence

  2. XR_241302.2 RNA Sequence

  3. XR_001738681.1 RNA Sequence

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