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Protein

Splicing factor 3B subunit 3

Gene

SF3B3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

  • protein complex binding Source: UniProtKB
  • RNA binding Source: GO_Central

GO - Biological processi

  • mRNA processing Source: ProtInc
  • mRNA splicing, via spliceosome Source: GO_Central
  • negative regulation of protein catabolic process Source: CACAO
  • protein complex assembly Source: ProtInc
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor 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
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:10770. SF3B3.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • nucleolus Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • small nuclear ribonucleoprotein complex Source: ProtInc
  • spliceosomal complex Source: ProtInc
  • U12-type spliceosomal complex Source: UniProtKB

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi23450.
OpenTargetsiENSG00000189091.
PharmGKBiPA35688.

Chemistry databases

ChEMBLiCHEMBL1250378.

Polymorphism and mutation databases

BioMutaiSF3B3.
DMDMi116242787.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002186391 – 1217Splicing factor 3B subunit 3Add BLAST1217

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei156PhosphoserineCombined sources1
Modified residuei1200PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ15393.
MaxQBiQ15393.
PaxDbiQ15393.
PeptideAtlasiQ15393.
PRIDEiQ15393.

PTM databases

iPTMnetiQ15393.
PhosphoSitePlusiQ15393.
SwissPalmiQ15393.

Expressioni

Gene expression databases

BgeeiENSG00000189091.
CleanExiHS_SAP130.
HS_SF3B3.
ExpressionAtlasiQ15393. baseline and differential.
GenevisibleiQ15393. HS.

Organism-specific databases

HPAiHPA041134.
HPA042986.

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

GO - Molecular functioni

  • protein complex binding Source: UniProtKB

Protein-protein interaction databases

BioGridi117016. 173 interactors.
DIPiDIP-28152N.
IntActiQ15393. 58 interactors.
MINTiMINT-1402891.
STRINGi9606.ENSP00000305790.

Chemistry databases

BindingDBiQ15393.

Structurei

Secondary structure

11217
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 9Combined sources7
Beta strandi15 – 20Combined sources6
Beta strandi24 – 26Combined sources3
Beta strandi29 – 33Combined sources5
Beta strandi35 – 43Combined sources9
Turni45 – 47Combined sources3
Beta strandi50 – 57Combined sources8
Beta strandi62 – 68Combined sources7
Beta strandi77 – 93Combined sources17
Turni94 – 97Combined sources4
Beta strandi98 – 106Combined sources9
Beta strandi110 – 112Combined sources3
Beta strandi114 – 117Combined sources4
Beta strandi119 – 123Combined sources5
Beta strandi127 – 133Combined sources7
Beta strandi135 – 137Combined sources3
Beta strandi139 – 146Combined sources8
Beta strandi152 – 154Combined sources3
Beta strandi165 – 173Combined sources9
Beta strandi176 – 179Combined sources4
Beta strandi181 – 188Combined sources8
Turni190 – 193Combined sources4
Turni199 – 203Combined sources5
Beta strandi207 – 214Combined sources8
Turni215 – 218Combined sources4
Beta strandi219 – 227Combined sources9
Beta strandi232 – 238Combined sources7
Beta strandi247 – 252Combined sources6
Beta strandi255 – 258Combined sources4
Beta strandi261 – 263Combined sources3
Beta strandi267 – 270Combined sources4
Beta strandi287 – 294Combined sources8
Beta strandi299 – 305Combined sources7
Beta strandi309 – 318Combined sources10
Beta strandi321 – 332Combined sources12
Beta strandi336 – 342Combined sources7
Turni343 – 345Combined sources3
Beta strandi346 – 354Combined sources9
Beta strandi356 – 361Combined sources6
Beta strandi367 – 370Combined sources4
Beta strandi372 – 374Combined sources3
Beta strandi393 – 401Combined sources9
Beta strandi406 – 413Combined sources8
Beta strandi416 – 420Combined sources5
Beta strandi422 – 427Combined sources6
Helixi430 – 432Combined sources3
Beta strandi434 – 442Combined sources9
Beta strandi445 – 451Combined sources7
Beta strandi458 – 462Combined sources5
Beta strandi473 – 477Combined sources5
Beta strandi482 – 486Combined sources5
Beta strandi488 – 490Combined sources3
Beta strandi506 – 510Combined sources5
Beta strandi512 – 514Combined sources3
Beta strandi516 – 520Combined sources5
Beta strandi523 – 527Combined sources5
Beta strandi529 – 531Combined sources3
Beta strandi533 – 537Combined sources5
Beta strandi544 – 549Combined sources6
Beta strandi551 – 558Combined sources8
Turni559 – 561Combined sources3
Beta strandi562 – 568Combined sources7
Beta strandi574 – 576Combined sources3
Beta strandi587 – 592Combined sources6
Beta strandi597 – 601Combined sources5
Beta strandi604 – 609Combined sources6
Beta strandi612 – 618Combined sources7
Helixi621 – 623Combined sources3
Beta strandi626 – 632Combined sources7
Beta strandi637 – 644Combined sources8
Beta strandi663 – 682Combined sources20
Beta strandi686 – 690Combined sources5
Beta strandi700 – 706Combined sources7
Beta strandi709 – 727Combined sources19
Beta strandi729 – 736Combined sources8
Beta strandi740 – 745Combined sources6
Beta strandi751 – 758Combined sources8
Beta strandi761 – 766Combined sources6
Beta strandi773 – 780Combined sources8
Beta strandi785 – 790Combined sources6
Turni792 – 794Combined sources3
Beta strandi797 – 804Combined sources8
Helixi809 – 824Combined sources16
Helixi839 – 842Combined sources4
Turni849 – 851Combined sources3
Beta strandi862 – 869Combined sources8
Beta strandi871 – 874Combined sources4
Beta strandi876 – 881Combined sources6
Beta strandi884 – 894Combined sources11
Beta strandi897 – 899Combined sources3
Beta strandi904 – 912Combined sources9
Turni915 – 918Combined sources4
Beta strandi922 – 928Combined sources7
Helixi931 – 934Combined sources4
Beta strandi939 – 947Combined sources9
Beta strandi949 – 955Combined sources7
Beta strandi958 – 963Combined sources6
Beta strandi966 – 971Combined sources6
Beta strandi974 – 976Combined sources3
Beta strandi978 – 983Combined sources6
Beta strandi990 – 994Combined sources5
Beta strandi997 – 1007Combined sources11
Beta strandi1009 – 1015Combined sources7
Turni1016 – 1019Combined sources4
Beta strandi1020 – 1029Combined sources10
Beta strandi1033 – 1038Combined sources6
Beta strandi1040 – 1048Combined sources9
Beta strandi1051 – 1057Combined sources7
Beta strandi1085 – 1096Combined sources12
Beta strandi1101 – 1110Combined sources10
Beta strandi1115 – 1121Combined sources7
Beta strandi1126 – 1129Combined sources4
Helixi1135 – 1151Combined sources17
Helixi1160 – 1164Combined sources5
Beta strandi1166 – 1168Combined sources3
Beta strandi1171 – 1175Combined sources5
Helixi1176 – 1179Combined sources4
Helixi1180 – 1184Combined sources5
Helixi1187 – 1196Combined sources10
Helixi1201 – 1215Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IFEX-ray3.10A1-1217[»]
ProteinModelPortaliQ15393.
SMRiQ15393.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RSE1 family.Curated

Phylogenomic databases

eggNOGiKOG1898. Eukaryota.
ENOG410XPFQ. LUCA.
GeneTreeiENSGT00530000063396.
HOGENOMiHOG000216677.
HOVERGENiHBG093942.
InParanoidiQ15393.
KOiK12830.
OMAiFACLEID.
OrthoDBiEOG091G00O8.
PhylomeDBiQ15393.
TreeFamiTF105685.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiView protein in InterPro
IPR004871. Cleavage/polyA-sp_fac_asu_C.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR017986. WD40_repeat_dom.
PfamiView protein in Pfam
PF03178. CPSF_A. 1 hit.
SUPFAMiSSF50978. SSF50978. 3 hits.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

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 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAA32662 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti193D → G in CAB56791 (PubMed:10490618).Curated1
Sequence conflicti301F → S in AAH68974 (PubMed:15489334).Curated1
Sequence conflicti302L → W in CAB56791 (PubMed:10490618).Curated1
Sequence conflicti899T → I in AAH00463 (PubMed:15489334).Curated1
Sequence conflicti899T → I in AAH03146 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_053647908G → R. Corresponds to variant dbSNP:rs11551673Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0229771 – 818Missing in isoform 3. 1 PublicationAdd BLAST818
Alternative sequenceiVSP_022978250 – 275ICSEN…IPRRR → NLSPPFPKAIPALICLDSPV YFCTHP in isoform 2. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_022979276 – 1217Missing in isoform 2. 1 PublicationAdd BLAST942

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IFEX-ray3.10A1-1217[»]
ProteinModelPortaliQ15393.
SMRiQ15393.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117016. 173 interactors.
DIPiDIP-28152N.
IntActiQ15393. 58 interactors.
MINTiMINT-1402891.
STRINGi9606.ENSP00000305790.

Chemistry databases

BindingDBiQ15393.
ChEMBLiCHEMBL1250378.

PTM databases

iPTMnetiQ15393.
PhosphoSitePlusiQ15393.
SwissPalmiQ15393.

Polymorphism and mutation databases

BioMutaiSF3B3.
DMDMi116242787.

Proteomic databases

EPDiQ15393.
MaxQBiQ15393.
PaxDbiQ15393.
PeptideAtlasiQ15393.
PRIDEiQ15393.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi23450.
DisGeNETi23450.
GeneCardsiSF3B3.
HGNCiHGNC:10770. SF3B3.
HPAiHPA041134.
HPA042986.
MIMi605592. gene.
neXtProtiNX_Q15393.
OpenTargetsiENSG00000189091.
PharmGKBiPA35688.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1898. Eukaryota.
ENOG410XPFQ. LUCA.
GeneTreeiENSGT00530000063396.
HOGENOMiHOG000216677.
HOVERGENiHBG093942.
InParanoidiQ15393.
KOiK12830.
OMAiFACLEID.
OrthoDBiEOG091G00O8.
PhylomeDBiQ15393.
TreeFamiTF105685.

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiSF3B3. human.
GeneWikiiSF3B3.
GenomeRNAii23450.
PROiPR:Q15393.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000189091.
CleanExiHS_SAP130.
HS_SF3B3.
ExpressionAtlasiQ15393. baseline and differential.
GenevisibleiQ15393. HS.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiView protein in InterPro
IPR004871. Cleavage/polyA-sp_fac_asu_C.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR017986. WD40_repeat_dom.
PfamiView protein in Pfam
PF03178. CPSF_A. 1 hit.
SUPFAMiSSF50978. SSF50978. 3 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiSF3B3_HUMAN
AccessioniPrimary (citable) accession number: Q15393
Secondary accession number(s): Q6NTI8
, Q96GC0, Q9BPY2, Q9UFX7, Q9UJ29
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: October 17, 2006
Last modified: June 7, 2017
This is version 169 of the entry and version 4 of the sequence. See 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

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.