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Aliases for SF3B1 Gene

Aliases for SF3B1 Gene

  • Splicing Factor 3b Subunit 1 2 3 5
  • Splicing Factor 3b, Subunit 1, 155kDa 2 3
  • Spliceosome-Associated Protein 155 3 4
  • SF3b155 3 4
  • SAP155 3 4
  • Pre-MRNA Splicing Factor SF3b, 155 KDa Subunit 3
  • Pre-MRNA-Splicing Factor SF3b 155 KDa Subunit 4
  • Splicing Factor 3b, Subunit 1, 155kD 2
  • Pre-MRNA Processing 10 3
  • SAP 155 4
  • Hsh155 3
  • PRPF10 3
  • PRP10 3
  • MDS 3

External Ids for SF3B1 Gene

Previous GeneCards Identifiers for SF3B1 Gene

  • GC02M196445
  • GC02M196969
  • GC02M198219
  • GC02M198459
  • GC02M198082
  • GC02M197964
  • GC02M198256
  • GC02M190109

Summaries for SF3B1 Gene

Entrez Gene Summary for SF3B1 Gene

  • 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]

CIViC summary for SF3B1 Gene

  • SF3B1 mutations have been described in several myeloid malignancies, predominantly myelodysplastic syndromes (MDS), as well as other hematologic malignancies, breast cancer, and uveal melanoma (UM). SF3B1 is one of several genes involved in RNA splicing that has been identified as recurrently mutated in MDS and other malignanices. The mutations affecting SF3B1 are typically heterozygous, point mutations suspected to be functionally deleterious with R625 and K700E described as a major mutation hotspots. MDS patients with SF3B1 mutations have been reported to have better overall and event-free survival than their wildtype counterparts. Additionally, these mutations are highly associated with subtypes of MDS characterized by ringed sideroblasts (refractory anemia with ringed sideroblasts and refractory cytopenia with multilineage dysplasia and ring sideroblasts). In UM patients, SF3B1 mutations have been reported to be associated with chromosome 3 disomy, which defines a subgroup with low risk of metastasis.

GeneCards Summary for SF3B1 Gene

SF3B1 (Splicing Factor 3b Subunit 1) is a Protein Coding gene. Diseases associated with SF3B1 include Myelodysplastic Syndrome and Acquired Idiopathic Sideroblastic Anemia. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and binding.

UniProtKB/Swiss-Prot for SF3B1 Gene

  • Subunit of the splicing factor SF3B required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the E complex. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Gene Wiki entry for SF3B1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B1 Gene

Genomics for SF3B1 Gene

Regulatory Elements for SF3B1 Gene

Enhancers for SF3B1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G197141 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.5 +293.2 293164 1.9 HDGF HCFC1 TAL1 BACH1 DPF2 TBX21 EP300 ARID1B ZNF143 RELB ANKRD44 SF3B1 LOC101927596 RNU6-1029P ENSG00000202434 MOB4 GC02P197128
GH02G197495 1.4 Ensembl ENCODE 11.2 -64.4 -64419 7.5 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 SP3 NPM1P46 RNU6-1029P SF3B1 ANKRD44 ENSG00000202434 PLCL1 COQ10B HSPE1 GC02P197477
GH02G197106 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +326.7 326668 3.2 MAX BMI1 RAD21 YY1 CTBP1 ZNF316 GATA2 FOS MAFK RFX1 ENSG00000202434 SF3B1 RNU6-1029P ANKRD44 GC02M197096 GC02P197128
GH02G197194 1.4 Ensembl ENCODE dbSUPER 9.4 +236.8 236812 8.4 HDGF TBP TBL1XR1 WRNIP1 SIN3A ZBTB40 TCF12 GATA2 EGR1 CBX5 ANKRD44-IT1 LOC105373824 ANKRD44 SF3B1 RNU6-1029P ENSG00000202434 MOB4 CCDC150 LOC101927596 LOC105373826
GH02G197143 1.3 Ensembl ENCODE dbSUPER 10.1 +289.9 289947 2.7 HDGF PKNOX1 ETV6 RELB IKZF2 CREM USF2 JUNB GATAD2B TBX21 ANKRD44 LOC101927596 ANKRD44-IT1 LOC105373824 SF3B1 RNU6-1029P ENSG00000202434 GC02P197128
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SF3B1 on UCSC Golden Path with GeneCards custom track

Promoters for SF3B1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000128436 491 2801 HDGF PKNOX1 MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9

Genomic Location for SF3B1 Gene

Chromosome:
2
Start:
197,389,784 bp from pter
End:
197,435,091 bp from pter
Size:
45,308 bases
Orientation:
Minus strand

Genomic View for SF3B1 Gene

Genes around SF3B1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3B1 Gene

Proteins for SF3B1 Gene

  • Protein details for SF3B1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75533-SF3B1_HUMAN
    Recommended name:
    Splicing factor 3B subunit 1
    Protein Accession:
    O75533
    Secondary Accessions:
    • E9PCH3

    Protein attributes for SF3B1 Gene

    Size:
    1304 amino acids
    Molecular mass:
    145830 Da
    Quaternary structure:
    • Interacts with SETX (PubMed:21700224). Identified in the spliceosome C complex. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Component of splicing factor SF3B which is composed of at least eight subunits; SF3B1/SAP155/SF3B155, SF3B2/SAP145/SF3B155, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42. Component of the B-WICH complex, at least composed of SMARCA5/SNF2H, BAZ1B/WSTF, SF3B1, DEK, MYO1C, ERCC6, MYBBP1A and DDX21. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). SF3B1 interacts directly with the splicing factor U2AF. Phosphorylated form interacts with PPP1R8. Interacts with PQBP1. Interacts with RBM17. Interacts with RBM39. Interacts with SF3B6 (PubMed:11991638, PubMed:12105215, PubMed:12234937, PubMed:12738865, PubMed:15146077, PubMed:16432215, PubMed:16603771, PubMed:17589525, PubMed:21062891, PubMed:23512658, PubMed:24795046).

    Three dimensional structures from OCA and Proteopedia for SF3B1 Gene

    Alternative splice isoforms for SF3B1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SF3B1 Gene

Post-translational modifications for SF3B1 Gene

  • Citrullinated by PADI4.
  • Phosphorylated. Phosphorylation occurs concomitantly with the splicing catalytic steps. Phosphorylation on Thr-244, Thr-248 and Thr-313 by cyclin-dependent kinases promotes interaction with PPP1R8 during mitosis.
  • Ubiquitination at isoforms=182, isoforms=195, Lys793, isoforms=816, isoforms=926, Lys1014, isoforms=1102, and Lys1292
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SF3B1 (SF3B1)

No data available for DME Specific Peptides for SF3B1 Gene

Domains & Families for SF3B1 Gene

Protein Domains for SF3B1 Gene

Graphical View of Domain Structure for InterPro Entry

O75533

UniProtKB/Swiss-Prot:

SF3B1_HUMAN :
  • Belongs to the SF3B1 family.
Family:
  • Belongs to the SF3B1 family.
genes like me logo Genes that share domains with SF3B1: view

No data available for Gene Families for SF3B1 Gene

Function for SF3B1 Gene

Molecular function for SF3B1 Gene

UniProtKB/Swiss-Prot Function:
Subunit of the splicing factor SF3B required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA. May also be involved in the assembly of the E complex. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.

Gene Ontology (GO) - Molecular Function for SF3B1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0003729 mRNA binding IBA --
GO:0005515 protein binding IPI 19515850
genes like me logo Genes that share ontologies with SF3B1: view
genes like me logo Genes that share phenotypes with SF3B1: view

Human Phenotype Ontology for SF3B1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SF3B1 Gene

MGI Knock Outs for SF3B1:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SF3B1

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SF3B1 Gene

Localization for SF3B1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B1 Gene

Nucleus speckle. Note=During mitosis, transiently dispersed from the nuclear speckles to the cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SF3B1 gene
Compartment Confidence
nucleus 5
plasma membrane 3
cytosol 1

Gene Ontology (GO) - Cellular Components for SF3B1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 18559850
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex NAS 9585501
GO:0005686 U2 snRNP IDA 11252167
GO:0005689 U12-type spliceosomal complex IDA 15146077
genes like me logo Genes that share ontologies with SF3B1: view

Pathways & Interactions for SF3B1 Gene

genes like me logo Genes that share pathways with SF3B1: view

Pathways by source for SF3B1 Gene

1 Cell Signaling Technology pathway for SF3B1 Gene
1 BioSystems pathway for SF3B1 Gene

SIGNOR curated interactions for SF3B1 Gene

Is activated by:
Other effect:

Gene Ontology (GO) - Biological Process for SF3B1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IBA --
GO:0000375 RNA splicing, via transesterification reactions NAS 9585501
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SF3B1: view

Transcripts for SF3B1 Gene

Unigene Clusters for SF3B1 Gene

Splicing factor 3b, subunit 1, 155kDa:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SF3B1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^
SP1: - - - -
SP2:
SP3:
SP4: - - -
SP5:
SP6: -
SP7:
SP8:
SP9:

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b · 24c ^ 25a · 25b
SP1:
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SF3B1 Gene

GeneLoc Exon Structure for
SF3B1
ECgene alternative splicing isoforms for
SF3B1

Expression for SF3B1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SF3B1 Gene

This gene is overexpressed in Tlymphocyte (8.3), Lymph node (7.5), and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SF3B1 Gene



Protein tissue co-expression partners for SF3B1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B1 Gene:

SF3B1

SOURCE GeneReport for Unigene cluster for SF3B1 Gene:

Hs.632554

Evidence on tissue expression from TISSUES for SF3B1 Gene

  • Nervous system(4.8)
  • Liver(4.5)
  • Intestine(3.2)
  • Heart(3.1)
  • Blood(2.9)
  • Lung(2.7)
  • Bone marrow(2.6)
  • Skin(2.6)
  • Thyroid gland(2.5)
  • Eye(2.4)
  • Lymph node(2.3)
  • Pancreas(2.3)
  • Adrenal gland(2.2)
  • Kidney(2.2)
  • Spleen(2.2)
  • Gall bladder(2.1)
  • Stomach(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3B1 Gene

Germ Layers:
  • mesoderm
Systems:
  • cardiovascular
Organs:
General:
  • blood
  • bone marrow
  • coagulation system
  • red blood cell
  • white blood cell
genes like me logo Genes that share expression patterns with SF3B1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SF3B1 Gene

Orthologs for SF3B1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SF3B1 34 35
  • 99.82 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3B1 35
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SF3B1 34 35
  • 95.55 (n)
cow
(Bos Taurus)
Mammalia SF3B1 34 35
  • 95.25 (n)
mouse
(Mus musculus)
Mammalia Sf3b1 34 16 35
  • 93.02 (n)
rat
(Rattus norvegicus)
Mammalia Sf3b1 34
  • 92.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 66 (a)
OneToMany
-- 35
  • 60 (a)
OneToMany
chicken
(Gallus gallus)
Aves SF3B1 34 35
  • 85.34 (n)
lizard
(Anolis carolinensis)
Reptilia SF3B1 35
  • 99 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sf3b1 34
  • 81.37 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2599 34
zebrafish
(Danio rerio)
Actinopterygii sf3b1 34 35
  • 78.67 (n)
wufb99f09 34
fruit fly
(Drosophila melanogaster)
Insecta CG2807 36 34 35
  • 68.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000178 34
  • 65.29 (n)
worm
(Caenorhabditis elegans)
Secernentea T08A11.2 34 35
  • 65.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HSH155 35 37
  • 50 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G64270 34
  • 66.61 (n)
soybean
(Glycine max)
eudicotyledons Gma.1115 34
rice
(Oryza sativa)
Liliopsida Os02g0147300 34
  • 65.38 (n)
Os.35337 34
wheat
(Triticum aestivum)
Liliopsida Ta.3352 34
corn
(Zea mays)
Liliopsida Zm.3656 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.683 35
  • 78 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp10 34
  • 62.82 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03042 34
  • 62.29 (n)
Species where no ortholog for SF3B1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SF3B1 Gene

ENSEMBL:
Gene Tree for SF3B1 (if available)
TreeFam:
Gene Tree for SF3B1 (if available)

Paralogs for SF3B1 Gene

(1) SIMAP similar genes for SF3B1 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with SF3B1: view

No data available for Paralogs for SF3B1 Gene

Variants for SF3B1 Gene

Sequence variations from dbSNP and Humsavar for SF3B1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs377023736 Pathogenic 197,402,635(+) ACAAT(A/C/G)TTAAT nc-transcript-variant, reference, missense
rs587778679 untested 197,408,519(-) ATTCT(A/G)TTGGT nc-transcript-variant, reference, missense
rs1000022158 -- 197,428,301(+) GGGTG(A/T)TAGAG intron-variant
rs1000044158 -- 197,395,206(+) TCACT(A/T)AGGAA intron-variant
rs1000117267 -- 197,433,602(+) TATAC(C/T)AATAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SF3B1 Gene

Variant ID Type Subtype PubMed ID
nsv1014881 CNV gain 25217958

Variation tolerance for SF3B1 Gene

Residual Variation Intolerance Score: 3.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.39; 8.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SF3B1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3B1 Gene

Disorders for SF3B1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SF3B1 Gene - From: OMIM, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
myelodysplastic syndrome
  • myelodysplastic syndrome, somatic
acquired idiopathic sideroblastic anemia
  • refractory anemia with ringed sideroblasts
uveal melanoma
  • melanoma of uvea
- elite association - COSMIC cancer census association via MalaCards
Search SF3B1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SF3B1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SF3B1
genes like me logo Genes that share disorders with SF3B1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SF3B1 Gene

Publications for SF3B1 Gene

  1. Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis. (PMID: 9585501) Wang C. … Reed R. (Genes Dev. 1998) 2 3 4 22 64
  2. Molecular architecture of the multiprotein splicing factor SF3b. (PMID: 12738865) Golas M.M. … Stark H. (Science 2003) 3 4 22 64
  3. Cancer-relevant splicing factor CAPERalpha engages the essential splicing factor SF3b155 in a specific ternary complex. (PMID: 24795046) Loerch S. … Kielkopf C.L. (J. Biol. Chem. 2014) 3 4 64
  4. Dimerization and protein binding specificity of the U2AF homology motif of the splicing factor Puf60. (PMID: 18974054) Corsini L. … Sattler M. (J. Biol. Chem. 2009) 3 22 64
  5. Nuclear inhibitor of protein phosphatase-1 (NIPP1) directs protein phosphatase-1 (PP1) to dephosphorylate the U2 small nuclear ribonucleoprotein particle (snRNP) component, spliceosome-associated protein 155 (Sap155). (PMID: 18842582) Tanuma N. … Shima H. (J. Biol. Chem. 2008) 3 22 64

Products for SF3B1 Gene

Sources for SF3B1 Gene

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