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Q15393

- SF3B3_HUMAN

UniProt

Q15393 - SF3B3_HUMAN

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Protein

Splicing factor 3B subunit 3

Gene

SF3B3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.

GO - Molecular functioni

  1. nucleic acid binding Source: InterPro

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA processing Source: ProtInc
  3. mRNA splicing, via spliceosome Source: UniProtKB
  4. protein complex assembly Source: ProtInc
  5. RNA splicing Source: Reactome
  6. RNA splicing, via transesterification reactions Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor 3B subunit 3
Alternative name(s):
Pre-mRNA-splicing factor SF3b 130 kDa subunit
Short name:
SF3b130
STAF130
Spliceosome-associated protein 130
Short name:
SAP 130
Gene namesi
Name:SF3B3
Synonyms:KIAA0017, SAP130
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 16

Organism-specific databases

HGNCiHGNC:10770. SF3B3.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. catalytic step 2 spliceosome Source: UniProtKB
  2. nucleoplasm Source: Reactome
  3. small nuclear ribonucleoprotein complex Source: ProtInc
  4. spliceosomal complex Source: ProtInc
  5. U12-type spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35688.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12171217Splicing factor 3B subunit 3PRO_0000218639Add
BLAST

Proteomic databases

MaxQBiQ15393.
PaxDbiQ15393.
PeptideAtlasiQ15393.
PRIDEiQ15393.

PTM databases

PhosphoSiteiQ15393.

Expressioni

Gene expression databases

BgeeiQ15393.
CleanExiHS_SAP130.
HS_SF3B3.
ExpressionAtlasiQ15393. baseline and differential.
GenevestigatoriQ15393.

Organism-specific databases

HPAiHPA042986.

Interactioni

Subunit structurei

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 complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42/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.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NUDCD3Q8IVD92EBI-346977,EBI-744342

Protein-protein interaction databases

BioGridi117016. 130 interactions.
DIPiDIP-28152N.
IntActiQ15393. 51 interactions.
MINTiMINT-1402891.
STRINGi9606.ENSP00000305790.

Structurei

3D structure databases

ProteinModelPortaliQ15393.
SMRiQ15393. Positions 438-769, 881-1211.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RSE1 family.Curated

Phylogenomic databases

eggNOGiNOG247734.
GeneTreeiENSGT00530000063396.
HOGENOMiHOG000216677.
HOVERGENiHBG093942.
InParanoidiQ15393.
KOiK12830.
OMAiHPKGIRH.
OrthoDBiEOG7N8ZTN.
PhylomeDBiQ15393.
TreeFamiTF105685.

Family and domain databases

InterProiIPR004871. Cleavage/polyA-sp_fac_asu_C.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF03178. CPSF_A. 1 hit.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 3 hits.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q15393-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV
60 70 80 90 100
HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVIL EYQPSKNMFE
110 120 130 140 150
KIHQETFGKS GCRRIVPGQF LAVDPKGRAV MISAIEKQKL VYILNRDAAA
160 170 180 190 200
RLTISSPLEA HKANTLVYHV VGVDVGFENP MFACLEMDYE EADNDPTGEA
210 220 230 240 250
AANTQQTLTF YELDLGLNHV VRKYSEPLEE HGNFLITVPG GSDGPSGVLI
260 270 280 290 300
CSENYITYKN FGDQPDIRCP IPRRRNDLDD PERGMIFVCS ATHKTKSMFF
310 320 330 340 350
FLAQTEQGDI FKITLETDED MVTEIRLKYF DTVPVAAAMC VLKTGFLFVA
360 370 380 390 400
SEFGNHYLYQ IAHLGDDDEE PEFSSAMPLE EGDTFFFQPR PLKNLVLVDE
410 420 430 440 450
LDSLSPILFC QIADLANEDT PQLYVACGRG PRSSLRVLRH GLEVSEMAVS
460 470 480 490 500
ELPGNPNAVW TVRRHIEDEF DAYIIVSFVN ATLVLSIGET VEEVTDSGFL
510 520 530 540 550
GTTPTLSCSL LGDDALVQVY PDGIRHIRAD KRVNEWKTPG KKTIVKCAVN
560 570 580 590 600
QRQVVIALTG GELVYFEMDP SGQLNEYTER KEMSADVVCM SLANVPPGEQ
610 620 630 640 650
RSRFLAVGLV DNTVRIISLD PSDCLQPLSM QALPAQPESL CIVEMGGTEK
660 670 680 690 700
QDELGERGSI GFLYLNIGLQ NGVLLRTVLD PVTGDLSDTR TRYLGSRPVK
710 720 730 740 750
LFRVRMQGQE AVLAMSSRSW LSYSYQSRFH LTPLSYETLE FASGFASEQC
760 770 780 790 800
PEGIVAISTN TLRILALEKL GAVFNQVAFP LQYTPRKFVI HPESNNLIII
810 820 830 840 850
ETDHNAYTEA TKAQRKQQMA EEMVEAAGED ERELAAEMAA AFLNENLPES
860 870 880 890 900
IFGAPKAGNG QWASVIRVMN PIQGNTLDLV QLEQNEAAFS VAVCRFSNTG
910 920 930 940 950
EDWYVLVGVA KDLILNPRSV AGGFVYTYKL VNNGEKLEFL HKTPVEEVPA
960 970 980 990 1000
AIAPFQGRVL IGVGKLLRVY DLGKKKLLRK CENKHIANYI SGIQTIGHRV
1010 1020 1030 1040 1050
IVSDVQESFI WVRYKRNENQ LIIFADDTYP RWVTTASLLD YDTVAGADKF
1060 1070 1080 1090 1100
GNICVVRLPP NTNDEVDEDP TGNKALWDRG LLNGASQKAE VIMNYHVGET
1110 1120 1130 1140 1150
VLSLQKTTLI PGGSESLVYT TLSGGIGILV PFTSHEDHDF FQHVEMHLRS
1160 1170 1180 1190 1200
EHPPLCGRDH LSFRSYYFPV KNVIDGDLCE QFNSMEPNKQ KNVSEELDRT
1210
PPEVSKKLED IRTRYAF
Length:1,217
Mass (Da):135,577
Last modified:October 17, 2006 - v4
Checksum:i35CACAF5ACC32512
GO
Isoform 2 (identifier: Q15393-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     250-275: ICSENYITYKNFGDQPDIRCPIPRRR → NLSPPFPKAIPALICLDSPVYFCTHP
     276-1217: Missing.

Note: No experimental confirmation available.

Show »
Length:275
Mass (Da):30,210
Checksum:iD46811A34E142E7D
GO
Isoform 3 (identifier: Q15393-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-818: Missing.

Note: No experimental confirmation available.

Show »
Length:399
Mass (Da):44,606
Checksum:iE8F6C071997055A0
GO

Sequence cautioni

The sequence BAA02805.1 differs from that shown. Reason: Erroneous initiation.
The sequence BAA32662.2 differs from that shown. Reason: Erroneous initiation.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti193 – 1931D → G in CAB56791. (PubMed:10490618)Curated
Sequence conflicti301 – 3011F → S in AAH68974. (PubMed:15489334)Curated
Sequence conflicti302 – 3021L → W in CAB56791. (PubMed:10490618)Curated
Sequence conflicti899 – 8991T → I in AAH00463. (PubMed:15489334)Curated
Sequence conflicti899 – 8991T → I in AAH03146. (PubMed:15489334)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti908 – 9081G → R.
Corresponds to variant rs11551673 [ dbSNP | Ensembl ].
VAR_053647

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 818818Missing in isoform 3. 1 PublicationVSP_022977Add
BLAST
Alternative sequencei250 – 27526ICSEN…IPRRR → NLSPPFPKAIPALICLDSPV YFCTHP in isoform 2. 1 PublicationVSP_022978Add
BLAST
Alternative sequencei276 – 1217942Missing in isoform 2. 1 PublicationVSP_022979Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ001443 mRNA. Translation: CAB56791.1.
D87686 mRNA. Translation: BAA32662.2. Different initiation.
D13642 mRNA. Translation: BAA02805.1. Different initiation.
BC000463 mRNA. Translation: AAH00463.1.
BC003146 mRNA. Translation: AAH03146.1.
BC009780 mRNA. Translation: AAH09780.1.
BC068974 mRNA. Translation: AAH68974.1.
AL110251 mRNA. Translation: CAB53699.1.
CCDSiCCDS10894.1. [Q15393-1]
PIRiT14779.
RefSeqiNP_036558.3. NM_012426.4. [Q15393-1]
UniGeneiHs.514435.

Genome annotation databases

EnsembliENST00000302516; ENSP00000305790; ENSG00000189091. [Q15393-1]
GeneIDi23450.
KEGGihsa:23450.
UCSCiuc002ezf.3. human. [Q15393-1]

Polymorphism databases

DMDMi116242787.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ001443 mRNA. Translation: CAB56791.1 .
D87686 mRNA. Translation: BAA32662.2 . Different initiation.
D13642 mRNA. Translation: BAA02805.1 . Different initiation.
BC000463 mRNA. Translation: AAH00463.1 .
BC003146 mRNA. Translation: AAH03146.1 .
BC009780 mRNA. Translation: AAH09780.1 .
BC068974 mRNA. Translation: AAH68974.1 .
AL110251 mRNA. Translation: CAB53699.1 .
CCDSi CCDS10894.1. [Q15393-1 ]
PIRi T14779.
RefSeqi NP_036558.3. NM_012426.4. [Q15393-1 ]
UniGenei Hs.514435.

3D structure databases

ProteinModelPortali Q15393.
SMRi Q15393. Positions 438-769, 881-1211.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 117016. 130 interactions.
DIPi DIP-28152N.
IntActi Q15393. 51 interactions.
MINTi MINT-1402891.
STRINGi 9606.ENSP00000305790.

Chemistry

BindingDBi Q15393.
ChEMBLi CHEMBL1250378.

PTM databases

PhosphoSitei Q15393.

Polymorphism databases

DMDMi 116242787.

Proteomic databases

MaxQBi Q15393.
PaxDbi Q15393.
PeptideAtlasi Q15393.
PRIDEi Q15393.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000302516 ; ENSP00000305790 ; ENSG00000189091 . [Q15393-1 ]
GeneIDi 23450.
KEGGi hsa:23450.
UCSCi uc002ezf.3. human. [Q15393-1 ]

Organism-specific databases

CTDi 23450.
GeneCardsi GC16P070557.
HGNCi HGNC:10770. SF3B3.
HPAi HPA042986.
MIMi 605592. gene.
neXtProti NX_Q15393.
PharmGKBi PA35688.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG247734.
GeneTreei ENSGT00530000063396.
HOGENOMi HOG000216677.
HOVERGENi HBG093942.
InParanoidi Q15393.
KOi K12830.
OMAi HPKGIRH.
OrthoDBi EOG7N8ZTN.
PhylomeDBi Q15393.
TreeFami TF105685.

Enzyme and pathway databases

Reactomei REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Miscellaneous databases

GeneWikii SF3B3.
GenomeRNAii 23450.
NextBioi 45731.
PROi Q15393.
SOURCEi Search...

Gene expression databases

Bgeei Q15393.
CleanExi HS_SAP130.
HS_SF3B3.
ExpressionAtlasi Q15393. baseline and differential.
Genevestigatori Q15393.

Family and domain databases

InterProi IPR004871. Cleavage/polyA-sp_fac_asu_C.
IPR017986. WD40_repeat_dom.
[Graphical view ]
Pfami PF03178. CPSF_A. 1 hit.
[Graphical view ]
SUPFAMi SSF50978. SSF50978. 3 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of a protein complex containing spliceosomal proteins saps 49,130,145 and 155."
    Das B.K., Xia L., Palandjian L., Gozani O., Chyung Y., Reed R.
    Mol. Cell. Biol. 19:6796-6802(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1."
    Nomura N., Miyajima N., Sazuka T., Tanaka A., Kawarabayasi Y., Sato S., Nagase T., Seki N., Ishikawa K., Tabata S.
    DNA Res. 1:27-35(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Bone marrow.
  3. Nomura N.
    Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
    Tissue: Lung, Skeletal muscle and Skin.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1003-1217 (ISOFORM 1).
    Tissue: Testis.
  6. "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo."
    Martinez E., Palhan V.B., Tjernberg A., Lymar E.S., Gamper A.M., Kundu T.K., Chait B.T., Roeder R.G.
    Mol. Cell. Biol. 21:6782-6795(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INTERACTION WITH SUPT3H, INTERACTION WITH THE STAGA COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "The TFIID components human TAFII140 and Drosophila BIP2 (TAFII155) are novel metazoan homologues of yeast TAFII47 containing a histone fold and a PHD finger."
    Gangloff Y.G., Pointud J.-C., Thuault S., Carre L., Romier C., Muratoglu S., Brand M., Tora L., Couderc J.-L., Davidson I.
    Mol. Cell. Biol. 21:5109-5121(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TAF3.
  8. "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein."
    Will C.L., Urlaub H., Achsel T., Gentzel M., Wilm M., Luehrmann R.
    EMBO J. 21:4978-4988(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SF3B COMPLEX.
  9. "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
    Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
    RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
  10. "Molecular architecture of the multiprotein splicing factor SF3b."
    Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H.
    Science 300:980-984(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SF3B COMPLEX, ELECTRON MICROSCOPY OF THE SF3B COMPLEX.
  11. "The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome."
    Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R.
    RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY MASS SPECTROMETRY.
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiSF3B3_HUMAN
AccessioniPrimary (citable) accession number: Q15393
Secondary accession number(s): Q6NTI8
, Q96GC0, Q9BPY2, Q9UFX7, Q9UJ29
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: October 17, 2006
Last modified: October 29, 2014
This is version 141 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3