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

    Gene ID: 23451, updated on 3-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
    mouse all
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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. SF3B1 Mutation but Not Ring Sideroblasts Identifies a Specific Group of Myelodysplastic Syndrome-Refractory Cytopenia With Multilineage Dysplasia. Xiong B, et al. Clin Lymphoma Myeloma Leuk, 2020 May. PMID 32037286
    2. MDS with deletions in the long arm of chromosome 11 are associated with a high frequency of SF3B1 mutations. Stengel A, et al. Leukemia, 2017 Sep. PMID 28592886
    3. Clonal trajectories and cellular dynamics of myeloid neoplasms with SF3B1 mutations. Awada H, et al. Leukemia, 2021 Nov. PMID 33603144, Free PMC Article
    4. Splicing factor mutations in MDS RARS and MDS/MPN-RS-T. Yoshimi A, et al. Int J Hematol, 2017 Jun. PMID 28466384
    5. SF3B1 is a stress-sensitive splicing factor that regulates both HSF1 concentration and activity. Kim Guisbert KS, et al. PLoS One, 2017. PMID 28445500, Free PMC Article

    See all (498) 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
    		Compare labs

    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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