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Aliases for SF3B3 Gene

Aliases for SF3B3 Gene

  • Splicing Factor 3b Subunit 3 2 3 5
  • Spliceosome-Associated Protein 130 3 4
  • SAP 130 3 4
  • SF3b130 3 4
  • STAF130 3 4
  • SAP130 3 4
  • Pre-MRNA Splicing Factor SF3b, 130 KDa Subunit 3
  • Pre-MRNA-Splicing Factor SF3b 130 KDa Subunit 4
  • Splicing Factor 3b, Subunit 3, 130kDa 2
  • Splicing Factor 3b, Subunit 3, 130kD 2
  • KIAA0017 4
  • RSE1 3

External Ids for SF3B3 Gene

Previous GeneCards Identifiers for SF3B3 Gene

  • GC16P061259
  • GC16P070978
  • GC16P070293
  • GC16P070333
  • GC16P069115
  • GC16P070557
  • GC16P056388

Summaries for SF3B3 Gene

Entrez Gene Summary for SF3B3 Gene

  • This gene encodes subunit 3 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. Subunit 3 has also been identified as a component of the STAGA (SPT3-TAF(II)31-GCN5L acetylase) transcription coactivator-HAT (histone acetyltransferase) complex, and the TFTC (TATA-binding-protein-free TAF(II)-containing complex). These complexes may function in chromatin modification, transcription, splicing, and DNA repair. [provided by RefSeq, Jul 2008]

GeneCards Summary for SF3B3 Gene

SF3B3 (Splicing Factor 3b Subunit 3) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is DDB1.

UniProtKB/Swiss-Prot for SF3B3 Gene

  • Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is 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 (PubMed:12234937). May also be involved in the assembly of the E complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077).

Gene Wiki entry for SF3B3 Gene

Additional gene information for SF3B3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B3 Gene

Genomics for SF3B3 Gene

GeneHancer (GH) Regulatory Elements for SF3B3 Gene

Promoters and enhancers for SF3B3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I070522 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 573.6 +0.3 279 3.5 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 SF3B3 COG4 PDXDC2P-NPIPB14P PDXDC2P NFAT5 NONOP1 DDX19B PDPR DDX19A ZNF23
GH16I070986 Enhancer 1.2 Ensembl ENCODE 77.7 +463.7 463674 1.1 PKNOX1 ZNF2 FOS KLF13 SP3 REST SMARCA4 GLIS1 NR2C1 NBN SF3B3 PDPR PDXDC2P-NPIPB14P DDX19A LOC400541 EXOSC6 HYDIN DDX19B NPIPB14P PDXDC2P
GH16I070287 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 33.8 -234.3 -234329 4.1 PKNOX1 SMAD1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B DDX19B AARS PDPR SMG1P7 NFAT5 NONOP1 SF3B3 COG4 LOC400541 DDX19A
GH16I070250 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.5 -272.3 -272254 2.7 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 EXOSC6 COG4 DDX19B NONOP1 SF3B3 PDPR NFAT5 PDXDC2P-NPIPB14P PDXDC2P NPIPB14P
GH16I069721 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.3 -798.5 -798536 7.2 CLOCK MLX DMAP1 SLC30A9 ZNF143 SP3 NFYC SSRP1 GLIS1 RCOR2 NQO1 ENSG00000262136 SNTB2 SF3B3 DDX19A NONOP1 CHTF8 NPIPB14P UTP4 PDPR
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SF3B3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SF3B3 gene promoter:

Genomic Locations for SF3B3 Gene

Genomic Locations for SF3B3 Gene
chr16:70,523,788-70,577,670
(GRCh38/hg38)
Size:
53,883 bases
Orientation:
Plus strand
chr16:70,557,691-70,611,571
(GRCh37/hg19)

Genomic View for SF3B3 Gene

Genes around SF3B3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3B3 Gene

Proteins for SF3B3 Gene

  • Protein details for SF3B3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15393-SF3B3_HUMAN
    Recommended name:
    Splicing factor 3B subunit 3
    Protein Accession:
    Q15393
    Secondary Accessions:
    • Q6NTI8
    • Q96GC0
    • Q9BPY2
    • Q9UFX7
    • Q9UJ29

    Protein attributes for SF3B3 Gene

    Size:
    1217 amino acids
    Molecular mass:
    135577 Da
    Quaternary structure:
    • Identified in the spliceosome C complex (PubMed:11991638). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42 (PubMed:12234937, PubMed:12738865, PubMed:28541300, PubMed:27720643). SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Interaction between SF3B3 and SF3B1 is tighter than the interaction between SF3B3 and SF3B2 (PubMed:12234937). Within the SF3B complex interacts directly with SF3B1 (via HEAT domain), SF3B5 and PHF5A (PubMed:27720643). The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2 (PubMed:27720643). Associates with the STAGA transcription coactivator-HAT complex. Interacts with SUPT3H (PubMed:11564863). Interacts with TAF3 (PubMed:11438666).
    SequenceCaution:
    • Sequence=BAA02805.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA32662.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SF3B3 Gene

    Alternative splice isoforms for SF3B3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SF3B3 Gene

Post-translational modifications for SF3B3 Gene

  • Ubiquitination at posLast=109109, posLast=139139, isoforms=546, isoforms=812, isoforms=3936, isoforms=3965, isoforms=31049, isoforms=31074, and isoforms=31171
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3B3 Gene

No data available for DME Specific Peptides for SF3B3 Gene

Domains & Families for SF3B3 Gene

Gene Families for SF3B3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SF3B3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q15393

UniProtKB/Swiss-Prot:

SF3B3_HUMAN :
  • The core of the protein consists of three beta-propeller domains.
  • Belongs to the RSE1 family.
Domain:
  • The core of the protein consists of three beta-propeller domains.
Family:
  • Belongs to the RSE1 family.
genes like me logo Genes that share domains with SF3B3: view

Function for SF3B3 Gene

Molecular function for SF3B3 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is 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 (PubMed:12234937). May also be involved in the assembly of the E complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077).

Phenotypes From GWAS Catalog for SF3B3 Gene

Gene Ontology (GO) - Molecular Function for SF3B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IBA --
GO:0005515 protein binding IPI 25036637
GO:0032403 protein complex binding IPI 11564863
genes like me logo Genes that share ontologies with SF3B3: view
genes like me logo Genes that share phenotypes with SF3B3: view

miRNA for SF3B3 Gene

miRTarBase miRNAs that target SF3B3

Clone Products

  • Addgene plasmids for SF3B3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3B3 Gene

Localization for SF3B3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B3 Gene

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 SF3B3 gene
Compartment Confidence
nucleus 5
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SF3B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex TAS 10490618
GO:0005689 U12-type spliceosomal complex IDA 15146077
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with SF3B3: view

Pathways & Interactions for SF3B3 Gene

genes like me logo Genes that share pathways with SF3B3: view

Pathways by source for SF3B3 Gene

1 KEGG pathway for SF3B3 Gene

Gene Ontology (GO) - Biological Process for SF3B3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 10490618
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing TAS 10490618
GO:0006461 protein complex assembly TAS 10490618
GO:0008380 RNA splicing TAS 10490618
genes like me logo Genes that share ontologies with SF3B3: view

No data available for SIGNOR curated interactions for SF3B3 Gene

Drugs & Compounds for SF3B3 Gene

(1) Drugs for SF3B3 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Quercetin Experimental, Investigational Nutra Target Antitumor agent 42
genes like me logo Genes that share compounds with SF3B3: view

Transcripts for SF3B3 Gene

Unigene Clusters for SF3B3 Gene

Splicing factor 3b, subunit 3, 130kDa:
Representative Sequences:

Clone Products

  • Addgene plasmids for SF3B3

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17 ^ 18a ·
SP1: - - -
SP2: -
SP3:
SP4: - - -
SP5: - -
SP6: - -
SP7: - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

ExUns: 18b ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b · 22c ^ 23a · 23b ^ 24a · 24b · 24c ^ 25 ^ 26a · 26b ^ 27 ^ 28a · 28b ^ 29 ^ 30a · 30b
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9: -
SP10:
SP11:
SP12:
SP13:

Relevant External Links for SF3B3 Gene

GeneLoc Exon Structure for
SF3B3
ECgene alternative splicing isoforms for
SF3B3

Expression for SF3B3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B3 Gene

Protein differential expression in normal tissues from HIPED for SF3B3 Gene

This gene is overexpressed in Lymph node (7.7) and Tlymphocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SF3B3 Gene



Protein tissue co-expression partners for SF3B3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B3 Gene:

SF3B3

SOURCE GeneReport for Unigene cluster for SF3B3 Gene:

Hs.514435

Evidence on tissue expression from TISSUES for SF3B3 Gene

  • Lung(4.7)
  • Nervous system(4.7)
  • Liver(4.6)
  • Bone marrow(4.3)
  • Muscle(4.3)
  • Skin(4.3)
  • Intestine(2.9)
  • Eye(2.4)
  • Heart(2.4)
genes like me logo Genes that share expression patterns with SF3B3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3B3 Gene

Orthologs for SF3B3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SF3B3 33 34
  • 99.67 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3B3 34
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SF3B3 33 34
  • 92.14 (n)
dog
(Canis familiaris)
Mammalia SF3B3 33 34
  • 92.08 (n)
rat
(Rattus norvegicus)
Mammalia Sf3b3 33
  • 90.91 (n)
mouse
(Mus musculus)
Mammalia Sf3b3 33 16 34
  • 90.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SF3B3 34
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves SF3B3 33 34
  • 82.74 (n)
lizard
(Anolis carolinensis)
Reptilia SF3B3 34
  • 99 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sf3b3 33
  • 79.29 (n)
Str.11469 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7617 33
zebrafish
(Danio rerio)
Actinopterygii sf3b3 34
  • 93 (a)
OneToOne
LOC100334114 33
  • 78.61 (n)
wufb81f05 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2859 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005549 33
  • 67.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG13900 35 33 34
  • 66.56 (n)
worm
(Caenorhabditis elegans)
Secernentea K02F2.3 35
  • 60 (a)
teg-4 33 34
  • 59.46 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RSE1 34 36
  • 20 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G55200 33
  • 59.86 (n)
rice
(Oryza sativa)
Liliopsida Os02g0137400 33
  • 57.68 (n)
Os.17819 33
barley
(Hordeum vulgare)
Liliopsida Hv.3072 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.949 34
  • 73 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU00396 33
  • 53.8 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp12 33
  • 50.7 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5102 33
Species where no ortholog for SF3B3 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)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SF3B3 Gene

ENSEMBL:
Gene Tree for SF3B3 (if available)
TreeFam:
Gene Tree for SF3B3 (if available)

Paralogs for SF3B3 Gene

Paralogs for SF3B3 Gene

genes like me logo Genes that share paralogs with SF3B3: view

Variants for SF3B3 Gene

Sequence variations from dbSNP and Humsavar for SF3B3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs193921118 uncertain-significance, Malignant tumor of prostate 70,554,544(+) G/T coding_sequence_variant, missense_variant
rs368602741 uncertain-significance, Congenital disorder of glycosylation 70,523,370(+) C/A/T upstream_transcript_variant
rs781200899 uncertain-significance, Congenital disorder of glycosylation 70,523,485(+) G/A/C upstream_transcript_variant
rs886052262 uncertain-significance, Congenital disorder of glycosylation 70,523,415(+) C/T upstream_transcript_variant
rs750500740 uncertain-significance, not specified 70,523,530(+) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SF3B3 Gene

Variant ID Type Subtype PubMed ID
esv3892881 CNV gain 25118596
esv3892883 CNV gain 25118596
nsv103855 CNV deletion 16902084
nsv475187 CNV novel sequence insertion 20440878
nsv7285 OTHER inversion 18451855
nsv833272 CNV loss 17160897

Variation tolerance for SF3B3 Gene

Residual Variation Intolerance Score: 2.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.47; 91.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3B3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3B3 Gene

Disorders for SF3B3 Gene

Additional Disease Information for SF3B3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SF3B3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SF3B3 Gene

Publications for SF3B3 Gene

  1. Characterization of a protein complex containing spliceosomal proteins SAPs 49, 130, 145, and 155. (PMID: 10490618) Das BK … Reed R (Molecular and cellular biology 1999) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will CL … Lührmann R (RNA (New York, N.Y.) 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PMID: 11991638) Jurica MS … Moore MJ (RNA (New York, N.Y.) 2002) 3 4 58

Products for SF3B3 Gene

  • Addgene plasmids for SF3B3

Sources for SF3B3 Gene

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