Human Gene SF3B3 (ENST00000302516.10_4) from GENCODE V47lift37
  Description: splicing factor 3b subunit 3 (from RefSeq NM_012426.5)
Gencode Transcript: ENST00000302516.10_4
Gencode Gene: ENSG00000189091.13_12
Transcript (Including UTRs)
   Position: hg19 chr16:70,557,719-70,611,571 Size: 53,853 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg19 chr16:70,560,560-70,605,716 Size: 45,157 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:70,557,719-70,611,571)mRNA (may differ from genome)Protein (1217 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SF3B3_HUMAN
DESCRIPTION: RecName: Full=Splicing factor 3B subunit 3; AltName: Full=Pre-mRNA-splicing factor SF3b 130 kDa subunit; Short=SF3b130; AltName: Full=STAF130; AltName: Full=Spliceosome-associated protein 130; Short=SAP 130;
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.
SUBUNIT: 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). Interaction between SF3B3 and SF3B1 is tighter than the interaction between SF3B3 and SF3B2. Associates with the STAGA transcription coactivator-HAT complex. Interacts with SUPT3H.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the RSE1 family.
SEQUENCE CAUTION: Sequence=BAA02805.1; Type=Erroneous initiation; Sequence=BAA32662.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.34 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 742.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -71.10183-0.389 Picture PostScript Text
3' UTR -2145.305855-0.366 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004871 - Cleavage/polyA-sp_fac_asu_C
IPR015943 - WD40/YVTN_repeat-like_dom

Pfam Domains:
PF03178 - CPSF A subunit region
PF10433 - Mono-functional DNA-alkylating methyl methanesulfonate N-term

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
101898 - NHL repeat
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q15393
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0044877 macromolecular complex binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0042177 negative regulation of protein catabolic process
GO:0071277 cellular response to calcium ion

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex
GO:0005730 nucleolus
GO:0030532 small nuclear ribonucleoprotein complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK291768 - Homo sapiens cDNA FLJ78677 complete cds, highly similar to Homo sapiens splicing factor 3b, subunit 3, 130kDa (SF3B3), mRNA.
BC009780 - Homo sapiens splicing factor 3b, subunit 3, 130kDa, mRNA (cDNA clone IMAGE:4293370), complete cds.
D87686 - Homo sapiens KIAA0017 mRNA for KIAA0017 protein.
AJ001443 - Homo sapiens mRNA for SAP 130 spliceosomal protein.
BC068974 - Homo sapiens splicing factor 3b, subunit 3, 130kDa, mRNA (cDNA clone MGC:74943 IMAGE:6168677), complete cds.
JD231940 - Sequence 212964 from Patent EP1572962.
AB383706 - Synthetic construct DNA, clone: pF1KSDA0017, Homo sapiens SF3B3 gene for splicing factor 3B subunit 3, complete cds, without stop codon, in Flexi system.
JF432652 - Synthetic construct Homo sapiens clone IMAGE:100073889 splicing factor 3b, subunit 3, 130kDa (SF3B3) gene, encodes complete protein.
KJ904692 - Synthetic construct Homo sapiens clone ccsbBroadEn_14086 SF3B3 gene, encodes complete protein.
AK074933 - Homo sapiens cDNA FLJ90452 fis, clone NT2RP3001475, highly similar to Splicing factor 3B subunit 3.
AK001297 - Homo sapiens cDNA FLJ10435 fis, clone NT2RP1000493, highly similar to Splicing factor 3B subunit 3.
D13642 - Homo sapiens KIAA0017 mRNA, complete cds.
CU674228 - Synthetic construct Homo sapiens gateway clone IMAGE:100018221 5' read SF3B3 mRNA.
KJ902342 - Synthetic construct Homo sapiens clone ccsbBroadEn_11736 SF3B3 gene, encodes complete protein.
BC000463 - Homo sapiens splicing factor 3b, subunit 3, 130kDa, mRNA (cDNA clone IMAGE:2822705), complete cds.
BC003146 - Homo sapiens splicing factor 3b, subunit 3, 130kDa, mRNA (cDNA clone IMAGE:2822705), complete cds.
AL110251 - Homo sapiens mRNA; cDNA DKFZp434P041 (from clone DKFZp434P041).
JD301251 - Sequence 282275 from Patent EP1572962.
JD121497 - Sequence 102521 from Patent EP1572962.
JD156640 - Sequence 137664 from Patent EP1572962.
JD188224 - Sequence 169248 from Patent EP1572962.
JD317716 - Sequence 298740 from Patent EP1572962.
JD131770 - Sequence 112794 from Patent EP1572962.
JD565187 - Sequence 546211 from Patent EP1572962.
JD116364 - Sequence 97388 from Patent EP1572962.
JD504071 - Sequence 485095 from Patent EP1572962.
JD427487 - Sequence 408511 from Patent EP1572962.
JD277226 - Sequence 258250 from Patent EP1572962.
JD177749 - Sequence 158773 from Patent EP1572962.
JD102388 - Sequence 83412 from Patent EP1572962.
JD480144 - Sequence 461168 from Patent EP1572962.
JD379774 - Sequence 360798 from Patent EP1572962.
JD365193 - Sequence 346217 from Patent EP1572962.
JD342502 - Sequence 323526 from Patent EP1572962.
JD480600 - Sequence 461624 from Patent EP1572962.
JD257308 - Sequence 238332 from Patent EP1572962.
JD488093 - Sequence 469117 from Patent EP1572962.
JD414695 - Sequence 395719 from Patent EP1572962.
JD306793 - Sequence 287817 from Patent EP1572962.
JD414697 - Sequence 395721 from Patent EP1572962.
LF208317 - JP 2014500723-A/15820: Polycomb-Associated Non-Coding RNAs.
LF374601 - JP 2014500723-A/182104: Polycomb-Associated Non-Coding RNAs.
JD065935 - Sequence 46959 from Patent EP1572962.
JD472478 - Sequence 453502 from Patent EP1572962.
JD533102 - Sequence 514126 from Patent EP1572962.
JD471569 - Sequence 452593 from Patent EP1572962.
MA443894 - JP 2018138019-A/15820: Polycomb-Associated Non-Coding RNAs.
MA610178 - JP 2018138019-A/182104: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q15393 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000302516.1, ENST00000302516.2, ENST00000302516.3, ENST00000302516.4, ENST00000302516.5, ENST00000302516.6, ENST00000302516.7, ENST00000302516.8, ENST00000302516.9, KIAA0017, NM_012426, Q15393, Q6NTI8, Q96GC0, Q9BPY2, Q9UFX7, Q9UJ29, SAP130 , SF3B3_HUMAN, uc317nbh.1, uc317nbh.2
UCSC ID: ENST00000302516.10_4
RefSeq Accession: NM_012426.5
Protein: Q15393 (aka SF3B3_HUMAN or S3B3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.