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

    Gene ID: 23451, updated on 8-Jul-2021

    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
    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

    See SF3B1 in Genome Data Viewer
    Location:
    2q33.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (197389784..197435093, complement)
    105.20201022 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 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Biological insights from 108 schizophrenia-associated genetic loci.
    GeneReviews: Not available
    Myelodysplastic syndrome
    MedGen: C3463824 OMIM: 614286 GeneReviews: Not available
    Compare labs

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables splicing factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    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
    PubMed 
    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
    PubMed 
    part_of U2 snRNP IDA
    Inferred from Direct Assay
    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
    PubMed 
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 
    part_of 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)

    NEW Try the new Transcript table

    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, ENST00000414963.2
    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, ENST00000487698.5
    3. NM_012433.4NP_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
      O75533
      UniProtKB/TrEMBL
      B4DGZ4
      Related
      ENSP00000335321.6, ENST00000335508.11
      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:332442
      SF3b1; Splicing factor 3B subunit 1

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      197389784..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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