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SF3B2 Gene(Protein Coding)

Splicing Factor 3b Subunit 2

GCID:
GC11P066050
GIFtS:
54
Genes Participants
UDN Logo

Aliases for SF3B2 Gene

Aliases for SF3B2 Gene

  • Splicing Factor 3b Subunit 2 2 3 5
  • Splicing Factor 3b, Subunit 2, 145kDa 2 3
  • Splicing Factor 3b, Subunit 2, 145kD 2 3
  • SAP 145 3 4
  • SF3B145 3 4
  • SF3b150 3 4
  • SAP145 3 4
  • Pre-MRNA Splicing Factor SF3b 145 KDa Subunit 3
  • Pre-MRNA-Splicing Factor SF3b 145 KDa Subunit 4
  • Spliceosome Associated Protein 145 3
  • Spliceosome-Associated Protein 145 4
  • SF3b1 3
  • Cus1 3

External Ids for SF3B2 Gene

Previous GeneCards Identifiers for SF3B2 Gene

  • GC11P068353
  • GC11P067501
  • GC11P066069
  • GC11P065594
  • GC11P065576
  • GC11P065825
  • GC11P065827
  • GC11P062145

Summaries for SF3B2 Gene

Entrez Gene Summary for SF3B2 Gene

  • This gene encodes subunit 2 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 2 associates with pre-mRNA upstream of the branch site at the anchoring site. Subunit 2 also interacts directly with subunit 4 of the splicing factor 3b complex. Subunit 2 is a highly hydrophilic protein with a proline-rich N-terminus and a glutamate-rich stretch in the C-terminus. [provided by RefSeq, Jul 2008]

GeneCards Summary for SF3B2 Gene

SF3B2 (Splicing Factor 3b Subunit 2) is a Protein Coding gene. Diseases associated with SF3B2 include Hiv-1. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding.

UniProtKB/Swiss-Prot for SF3B2 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 SF3B2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B2 Gene

Genomics for SF3B2 Gene

Products:

  1. Regulatory Element

Regulatory Elements for SF3B2 Gene

Enhancers for SF3B2 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
GH11G066078 1.9 FANTOM5 Ensembl ENCODE dbSUPER 21.9 +31.1 31081 7.5 HDGF PKNOX1 FOXA2 AGO1 SIN3A YBX1 FEZF1 ZNF121 GATA2 CBX5 EIF1AD ENSG00000255320 SF3B2 SIPA1 RBM14 PACS1 ENSG00000258297 ZFPL1 PCNX3 KAT5
GH11G066111 1.7 Ensembl ENCODE dbSUPER 22.1 +65.4 65437 10.3 HNRNPUL1 HDGF PKNOX1 FOXA2 CREB3L1 AGO1 WRNIP1 ARID4B SIN3A DMAP1 EIF1AD RBM14 ENSG00000255320 ENSG00000258297 SF3B2 ENSG00000255038 PACS1 LOC105369352 RBM4B KLC2
GH11G066099 1.4 Ensembl ENCODE dbSUPER 21.3 +50.5 50451 3.0 HDGF PKNOX1 AGO1 YY1 GLIS2 SCRT2 ZNF143 THAP11 DEK ZNF263 SF3B2 ENSG00000255320 ENSG00000255038 PACS1 CST6 BANF1 EIF1AD RAB1B ENSG00000254461 LOC105369352
GH11G066050 1.1 ENCODE 20.3 +1.5 1528 3.1 HDGF PKNOX1 ARNT CREB3L1 MLX AGO1 ARID4B SIN3A FEZF1 DMAP1 SF3B2 CATSPER1 KLC2 TMEM151A GC11P066062
GH11G066135 1.8 FANTOM5 Ensembl ENCODE dbSUPER 10.5 +86.4 86441 2.4 HDGF PKNOX1 FOXA2 ATF1 WRNIP1 ARID4B GLIS2 CBX5 ZNF143 ZNF207 PACS1 ENSG00000255038 ENSG00000254461 KLC2 ENSG00000255320 SF3B2 CST6 EIF1AD BANF1 TMEM151A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SF3B2 on UCSC Golden Path with GeneCards custom track

Promoters for SF3B2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040926 1671 1601 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1

Transcription factor binding sites by QIAGEN in the SF3B2 gene promoter:

Genomic Location for SF3B2 Gene

Chromosome:
11
Start:
66,050,729 bp from pter
End:
66,069,308 bp from pter
Size:
18,580 bases
Orientation:
Plus strand

Genomic View for SF3B2 Gene

Genes around SF3B2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SF3B2 Gene

Proteins for SF3B2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SF3B2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13435-SF3B2_HUMAN
    Recommended name:
    Splicing factor 3B subunit 2
    Protein Accession:
    Q13435
    Secondary Accessions:
    • A8K485
    • B4DT19
    • Q7L4T5
    • Q7Z627
    • Q969K1
    • Q96CM6
    • Q9BWD2

    Protein attributes for SF3B2 Gene

    Size:
    895 amino acids
    Molecular mass:
    100228 Da
    Quaternary structure:
    • 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/SF3B145, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B14A, PHF5A/SF3B14B, SF3B10 and SF3B125. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). SF3B2 interacts directly with SF3B4. Interacts with HIV-1 Vpr.
    SequenceCaution:
    • Sequence=AAA97461.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAA97461.1; Type=Frameshift; Positions=28; Evidence={ECO:0000305}; Sequence=AAH53577.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAG61831.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SF3B2 Gene

neXtProt entry for SF3B2 Gene

Protein Expression for SF3B2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SF3B2 Gene

  • Ubiquitination at isoforms=280, Lys466, isoforms=486, isoforms=492, isoforms=529, isoforms=570, isoforms=577, and isoforms=790
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3B2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SF3B2 Gene

Domains & Families for SF3B2 Gene

Protein Domains for SF3B2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SF3B2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SF3B2: view

No data available for Gene Families and UniProtKB/Swiss-Prot for SF3B2 Gene

Function for SF3B2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for SF3B2 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 SF3B2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with SF3B2: view
genes like me logo Genes that share phenotypes with SF3B2: view

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SF3B2

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3B2 Gene

Localization for SF3B2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B2 Gene

Nucleus.

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 SF3B2 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for SF3B2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0005684 U2-type spliceosomal complex IBA --
GO:0005686 U2 snRNP IBA --
genes like me logo Genes that share ontologies with SF3B2: view

Pathways & Interactions for SF3B2 Gene

genes like me logo Genes that share pathways with SF3B2: view

Pathways by source for SF3B2 Gene

1 BioSystems pathway for SF3B2 Gene
1 KEGG pathway for SF3B2 Gene

Gene Ontology (GO) - Biological Process for SF3B2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing TAS 8566756
GO:0008380 RNA splicing TAS 8566756
GO:0016032 viral process IEA --
genes like me logo Genes that share ontologies with SF3B2: view

No data available for SIGNOR curated interactions for SF3B2 Gene

Drugs & Compounds for SF3B2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SF3B2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for SF3B2 Gene

(4) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(854) Selected AceView cDNA sequences:
(16) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SF3B2 Gene

Splicing factor 3b, subunit 2, 145kDa:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SF3B2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ^ 11 ^ 12 ^ 13a ·
SP1: - - -
SP2: - - - - - - -
SP3: -
SP4: -
SP5: - - -
SP6: - - -
SP7:
SP8:
SP9:
SP10: -
SP11:

ExUns: 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22a · 22b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SF3B2 Gene

GeneLoc Exon Structure for
SF3B2
ECgene alternative splicing isoforms for
SF3B2

Expression for SF3B2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B2 Gene

mRNA expression in normal human tissues for SF3B2 Gene
mRNA expression by BioGPS for SF3B2 GenemRNA expression by GTEx for SF3B2 Gene

Protein differential expression in normal tissues from HIPED for SF3B2 Gene

This gene is overexpressed in Nasal epithelium (9.2) and Peripheral blood mononuclear cells (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SF3B2 Gene



Protein tissue co-expression partners for SF3B2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B2 Gene:

SF3B2

SOURCE GeneReport for Unigene cluster for SF3B2 Gene:

Hs.406423

Evidence on tissue expression from TISSUES for SF3B2 Gene

  • Eye(4.8)
  • Lung(4.8)
  • Liver(4.6)
  • Blood(4.5)
  • Kidney(4.4)
  • Nervous system(4.3)
  • Intestine(2.8)
  • Skin(2.8)
  • Thyroid gland(2.7)
  • Pancreas(2.5)
  • Heart(2.1)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with SF3B2: view

Primer Products

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 SF3B2 Gene

Orthologs for SF3B2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SF3B2 34 35
  • 99.81 (n)
dog
(Canis familiaris)
 Mammalia SF3B2 34 35
  • 92.86 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 35
  • 92 (a)
 OneToMany
-- 35
  • 90 (a)
 OneToMany
cow
(Bos Taurus)
 Mammalia SF3B2 34 35
  • 91.52 (n)
rat
(Rattus norvegicus)
 Mammalia Sf3b2 34
  • 89.79 (n)
mouse
(Mus musculus)
 Mammalia Sf3b2 34 16 35
  • 89.67 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SF3B2 35
  • 83 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SF3B2 35
  • 67 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia sf3b2 34
  • 71.83 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.6684 34
zebrafish
(Danio rerio)
 Actinopterygii sf3b2 34 35
  • 72.28 (n)
wufb53c07 34
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.9085 34
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006240 34
  • 64.68 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG3605 36 34 35
  • 63.55 (n)
worm
(Caenorhabditis elegans)
 Secernentea CELE_W03F9.10 34
  • 57.79 (n)
W03F9.10 36 35
  • 50 (a)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes CUS1 35 37
  • 30 (a)
 OneToOne
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT4G21660 34
  • 56.47 (n)
rice
(Oryza sativa)
 Liliopsida Os02g0827300 34
  • 55.92 (n)
Os.26501 34
barley
(Hordeum vulgare)
 Liliopsida Hv.9620 34
corn
(Zea mays)
 Liliopsida Zm.837 34
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.10434 35
  • 62 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.160 34
Species where no ortholog for SF3B2 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)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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 SF3B2 Gene

ENSEMBL:
Gene Tree for SF3B2 (if available)
TreeFam:
Gene Tree for SF3B2 (if available)

Paralogs for SF3B2 Gene

(1) SIMAP similar genes for SF3B2 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with SF3B2: view

No data available for Paralogs for SF3B2 Gene

Variants for SF3B2 Gene

Sequence variations from dbSNP and Humsavar for SF3B2 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000004252 -- 66,065,633(+) AAGAG(C/T)TCACT intron-variant
rs1000119972 -- 66,065,308(+) GTCTT(C/T)TTTCT intron-variant
rs1000122418 -- 66,054,829(+) GTCTC(C/T)TAGAA intron-variant
rs1001111307 -- 66,051,798(+) CAGGC(C/T)TGCTG upstream-variant-2KB, utr-variant-5-prime
rs1001132754 -- 66,066,017(+) ATAGG(C/T)GTGCG intron-variant

Variation tolerance for SF3B2 Gene

Residual Variation Intolerance Score: 4.77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.60; 56.31% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SF3B2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SF3B2 Gene

Disorders for SF3B2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SF3B2 Gene - From: GeneCards

Disorder Aliases PubMed IDs
hiv-1
  • aids, slow progression to
- elite association - COSMIC cancer census association via MalaCards
Search SF3B2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SF3B2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SF3B2
genes like me logo Genes that share disorders with SF3B2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SF3B2 Gene

Publications for SF3B2 Gene

  1. Human immunodeficiency virus type 1 Vpr induces G2 checkpoint activation by interacting with the splicing factor SAP145. (PMID: 16923959) Terada Y. … Yasuda Y. (Mol. Cell. Biol. 2006) 3 4 22 64
  2. Evidence that sequence-independent binding of highly conserved U2 snRNP proteins upstream of the branch site is required for assembly of spliceosomal complex A. (PMID: 8566756) Gozani O. … Reed R. (Genes Dev. 1996) 2 3 4 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  4. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will C.L. … Luehrmann R. (RNA 2004) 3 4 64
  5. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PMID: 11991638) Jurica M.S. … Moore M.J. (RNA 2002) 3 4 64

Products for SF3B2 Gene

  • Addgene plasmids for SF3B2

Sources for SF3B2 Gene

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