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Protein

Splicing factor 3B subunit 1

Gene

SF3B1

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

  • mRNA binding Source: GO_Central
  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA splicing, via spliceosome Source: MGI
  • positive regulation of gene expression, epigenetic Source: Reactome
  • RNA splicing, via transesterification reactions Source: UniProtKB
  • spliceosomal complex assembly Source: GO_Central

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-5250924. B-WICH complex positively regulates rRNA expression.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
SIGNORiO75533.

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor 3B subunit 1
Alternative name(s):
Pre-mRNA-splicing factor SF3b 155 kDa subunit
Short name:
SF3b155
Spliceosome-associated protein 155
Short name:
SAP 155
Gene namesi
Name:SF3B1
Synonyms:SAP155
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000115524.15.
HGNCiHGNC:10768. SF3B1.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi200W → A: Abolishes interaction with RBM39; when associated with A-218; A-232; A-254; A-293; A-310 and A-338. 1 Publication1
Mutagenesisi218W → A: Abolishes interaction with RBM39; when associated with A-200; A-232; A-254; A-293; A-310 and A-338. 1 Publication1
Mutagenesisi223T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi227T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi232W → A: Abolishes interaction with RBM39; when associated with A-200; A-218; A-254; A-293; A-310 and A-338. 1 Publication1
Mutagenesisi235T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi244T → A: Slight inhibition of interaction with PPP1R8. 1 Publication1
Mutagenesisi248T → A: Slight inhibition of interaction with PPP1R8. 1 Publication1
Mutagenesisi254W → A: Abolishes interaction with RBM39; when associated with A-200; A-218; A-232; A-293; A-310 and A-338. 1 Publication1
Mutagenesisi257T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi261T → A: Slight inhibition of interaction with PPP1R8. 1 Publication1
Mutagenesisi267T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi273T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi278T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi293W → A: Abolishes interaction with RBM39; when associated with A-200; A-218; A-232; A-254; A-310 and A-338. 1 Publication1
Mutagenesisi296T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi303T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi310W → A: Abolishes interaction with RBM39; when associated with A-200; A-218; A-232; A-254; A-293 and A-338. 1 Publication1
Mutagenesisi313T → A: No effect on interaction with PPP1R8. 1 Publication1
Mutagenesisi338W → A: Abolishes interaction with RBM39; when associated with A-200; A-218; A-232; A-254; A-293 and A-310. 1 Publication1

Organism-specific databases

DisGeNETi23451.
MalaCardsiSF3B1.
OpenTargetsiENSG00000115524.
Orphaneti75564. Acquired idiopathic sideroblastic anemia.
PharmGKBiPA35686.

Polymorphism and mutation databases

BioMutaiSF3B1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001743231 – 1304Splicing factor 3B subunit 1Add BLAST1304

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei125PhosphothreonineCombined sources1
Modified residuei129PhosphoserineCombined sources1
Modified residuei141N6-acetyllysineCombined sources1
Modified residuei142PhosphothreonineCombined sources1
Modified residuei157CitrullineBy similarity1
Modified residuei194PhosphoserineCombined sources1
Modified residuei203PhosphothreonineCombined sources1
Modified residuei207PhosphothreonineCombined sources1
Modified residuei211PhosphothreonineCombined sources1
Modified residuei214N6-acetyllysine; alternateBy similarity1
Cross-linki214Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei223PhosphothreonineCombined sources1
Modified residuei227PhosphothreonineCombined sources1
Modified residuei229PhosphoserineBy similarity1
Modified residuei235PhosphothreonineCombined sources1
Modified residuei244Phosphothreonine1 Publication1
Modified residuei248Phosphothreonine1 Publication1
Modified residuei257PhosphothreonineCombined sources1
Modified residuei261PhosphothreonineCombined sources1
Modified residuei267PhosphothreonineCombined sources1
Modified residuei273PhosphothreonineCombined sources1
Modified residuei278PhosphothreonineCombined sources1
Modified residuei287PhosphoserineCombined sources1
Modified residuei296PhosphothreonineCombined sources1
Modified residuei299PhosphothreonineCombined sources1
Modified residuei303PhosphothreonineCombined sources1
Modified residuei313PhosphothreonineCombined sources1
Modified residuei322PhosphoserineCombined sources1
Modified residuei326PhosphothreonineCombined sources1
Modified residuei328PhosphothreonineCombined sources1
Modified residuei332PhosphoserineCombined sources1
Modified residuei341PhosphothreonineCombined sources1
Modified residuei344PhosphoserineCombined sources1
Modified residuei349PhosphoserineCombined sources1
Modified residuei350PhosphothreonineCombined sources1
Modified residuei354PhosphothreonineCombined sources1
Modified residuei400PhosphoserineCombined sources1
Cross-linki413Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Cross-linki413Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei426PhosphothreonineCombined sources1
Cross-linki430Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei434PhosphothreonineCombined sources1
Modified residuei436PhosphothreonineCombined sources1
Modified residuei488PhosphoserineCombined sources1
Modified residuei554N6-acetyllysineCombined sources1
Modified residuei562N6-acetyllysineCombined sources1

Post-translational modificationi

Phosphorylated. Phosphorylation occurs concomitantly with the splicing catalytic steps. Phosphorylation on Thr-244, Thr-248 and Thr-313 by cyclin-dependent kinases promotes interaction with PPP1R8 during mitosis.2 Publications
Citrullinated by PADI4.By similarity

Keywords - PTMi

Acetylation, Citrullination, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO75533.
MaxQBiO75533.
PaxDbiO75533.
PeptideAtlasiO75533.
PRIDEiO75533.

PTM databases

iPTMnetiO75533.
PhosphoSitePlusiO75533.
SwissPalmiO75533.

Miscellaneous databases

PMAP-CutDBiO75533.

Expressioni

Gene expression databases

BgeeiENSG00000115524.
CleanExiHS_SF3B1.
ExpressionAtlasiO75533. baseline and differential.
GenevisibleiO75533. HS.

Organism-specific databases

HPAiHPA050275.

Interactioni

Subunit structurei

Interacts with SETX (PubMed:21700224). 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/SF3B155, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42. Component of the B-WICH complex, at least composed of SMARCA5/SNF2H, BAZ1B/WSTF, SF3B1, DEK, MYO1C, ERCC6, MYBBP1A and DDX21. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). SF3B1 interacts directly with the splicing factor U2AF. Phosphorylated form interacts with PPP1R8. Interacts with PQBP1. Interacts with RBM17. Interacts with RBM39. Interacts with SF3B6 (PubMed:11991638, PubMed:12105215, PubMed:12234937, PubMed:12738865, PubMed:15146077, PubMed:16432215, PubMed:16603771, PubMed:17589525, PubMed:21062891, PubMed:23512658, PubMed:24795046).12 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RBM17Q96I252EBI-876542,EBI-740272

Protein-protein interaction databases

BioGridi117017. 196 interactors.
CORUMiO75533.
DIPiDIP-29411N.
ELMiO75533.
IntActiO75533. 79 interactors.
MINTiMINT-1185911.
STRINGi9606.ENSP00000335321.

Structurei

Secondary structure

11304
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi380 – 394Combined sources15
Helixi401 – 406Combined sources6
Beta strandi410 – 414Combined sources5
Helixi469 – 471Combined sources3
Helixi472 – 475Combined sources4
Helixi476 – 478Combined sources3
Helixi491 – 498Combined sources8
Helixi500 – 505Combined sources6
Helixi509 – 521Combined sources13
Helixi523 – 526Combined sources4
Helixi528 – 540Combined sources13
Helixi546 – 562Combined sources17
Helixi568 – 570Combined sources3
Helixi571 – 578Combined sources8
Helixi579 – 583Combined sources5
Helixi587 – 603Combined sources17
Helixi606 – 613Combined sources8
Turni615 – 618Combined sources4
Helixi622 – 639Combined sources18
Helixi641 – 651Combined sources11
Helixi658 – 675Combined sources18
Helixi676 – 682Combined sources7
Helixi683 – 690Combined sources8
Helixi691 – 695Combined sources5
Helixi699 – 716Combined sources18
Helixi722 – 724Combined sources3
Helixi725 – 737Combined sources13
Helixi741 – 753Combined sources13
Helixi754 – 756Combined sources3
Helixi759 – 775Combined sources17
Helixi776 – 778Combined sources3
Helixi782 – 795Combined sources14
Beta strandi798 – 801Combined sources4
Helixi803 – 809Combined sources7
Helixi811 – 817Combined sources7
Helixi821 – 823Combined sources3
Helixi827 – 844Combined sources18
Helixi846 – 854Combined sources9
Helixi855 – 858Combined sources4
Helixi862 – 879Combined sources18
Helixi886 – 901Combined sources16
Helixi908 – 921Combined sources14
Helixi922 – 928Combined sources7
Helixi929 – 940Combined sources12
Helixi948 – 963Combined sources16
Turni964 – 966Combined sources3
Helixi968 – 979Combined sources12
Turni980 – 983Combined sources4
Helixi987 – 1001Combined sources15
Helixi1013 – 1020Combined sources8
Helixi1021 – 1025Combined sources5
Helixi1029 – 1045Combined sources17
Helixi1047 – 1049Combined sources3
Helixi1052 – 1062Combined sources11
Helixi1063 – 1067Combined sources5
Helixi1071 – 1088Combined sources18
Helixi1109 – 1122Combined sources14
Turni1125 – 1128Combined sources4
Helixi1129 – 1134Combined sources6
Beta strandi1137 – 1139Combined sources3
Helixi1141 – 1158Combined sources18
Helixi1159 – 1164Combined sources6
Helixi1166 – 1177Combined sources12
Beta strandi1178 – 1180Combined sources3
Helixi1182 – 1199Combined sources18
Helixi1205 – 1215Combined sources11
Helixi1216 – 1219Combined sources4
Helixi1224 – 1241Combined sources18
Helixi1243 – 1250Combined sources8
Helixi1252 – 1254Combined sources3
Helixi1259 – 1274Combined sources16
Turni1277 – 1279Combined sources3
Helixi1280 – 1282Combined sources3
Helixi1299 – 1301Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2F9DX-ray2.50P/Q373-415[»]
2F9JX-ray3.00P/Q380-415[»]
2FHONMR-A379-424[»]
2PEHX-ray2.11C/D333-342[»]
3LQVX-ray2.38P/Q377-415[»]
4OZ1X-ray1.74C333-342[»]
5IFEX-ray3.10C1-1304[»]
ProteinModelPortaliO75533.
SMRiO75533.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO75533.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati529 – 568HEAT 1Add BLAST40
Repeati569 – 603HEAT 2Add BLAST35
Repeati604 – 641HEAT 3Add BLAST38
Repeati643 – 677HEAT 4Add BLAST35
Repeati680 – 718HEAT 5Add BLAST39
Repeati763 – 801HEAT 6Add BLAST39
Repeati843 – 881HEAT 7Add BLAST39
Repeati1010 – 1048HEAT 8Add BLAST39
Repeati1052 – 1090HEAT 9Add BLAST39
Repeati1122 – 1160HEAT 10Add BLAST39
Repeati1163 – 1201HEAT 11Add BLAST39

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni190 – 342U2AF homology region; mediates interaction with RBM391 PublicationAdd BLAST153
Regioni223 – 491Interaction with PPP1R81 PublicationAdd BLAST269
Regioni529 – 568Interaction with SF3B14Add BLAST40

Sequence similaritiesi

Belongs to the SF3B1 family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0213. Eukaryota.
COG5181. LUCA.
GeneTreeiENSGT00390000018393.
HOGENOMiHOG000166737.
HOVERGENiHBG079173.
InParanoidiO75533.
KOiK12828.
OMAiYAVCPLL.
OrthoDBiEOG091G00Q0.
PhylomeDBiO75533.
TreeFamiTF105680.

Family and domain databases

Gene3Di1.25.10.10. 2 hits.
InterProiView protein in InterPro
IPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR015016. SF3b_su1.
PfamiView protein in Pfam
PF08920. SF3b1. 1 hit.
SUPFAMiSSF48371. SSF48371. 3 hits.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O75533-1) [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
MAKIAKTHED IEAQIREIQG KKAALDEAQG VGLDSTGYYD QEIYGGSDSR
60 70 80 90 100
FAGYVTSIAA TELEDDDDDY SSSTSLLGQK KPGYHAPVAL LNDIPQSTEQ
110 120 130 140 150
YDPFAEHRPP KIADREDEYK KHRRTMIISP ERLDPFADGG KTPDPKMNAR
160 170 180 190 200
TYMDVMREQH LTKEEREIRQ QLAEKAKAGE LKVVNGAAAS QPPSKRKRRW
210 220 230 240 250
DQTADQTPGA TPKKLSSWDQ AETPGHTPSL RWDETPGRAK GSETPGATPG
260 270 280 290 300
SKIWDPTPSH TPAGAATPGR GDTPGHATPG HGGATSSARK NRWDETPKTE
310 320 330 340 350
RDTPGHGSGW AETPRTDRGG DSIGETPTPG ASKRKSRWDE TPASQMGGST
360 370 380 390 400
PVLTPGKTPI GTPAMNMATP TPGHIMSMTP EQLQAWRWER EIDERNRPLS
410 420 430 440 450
DEELDAMFPE GYKVLPPPAG YVPIRTPARK LTATPTPLGG MTGFHMQTED
460 470 480 490 500
RTMKSVNDQP SGNLPFLKPD DIQYFDKLLV DVDESTLSPE EQKERKIMKL
510 520 530 540 550
LLKIKNGTPP MRKAALRQIT DKAREFGAGP LFNQILPLLM SPTLEDQERH
560 570 580 590 600
LLVKVIDRIL YKLDDLVRPY VHKILVVIEP LLIDEDYYAR VEGREIISNL
610 620 630 640 650
AKAAGLATMI STMRPDIDNM DEYVRNTTAR AFAVVASALG IPSLLPFLKA
660 670 680 690 700
VCKSKKSWQA RHTGIKIVQQ IAILMGCAIL PHLRSLVEII EHGLVDEQQK
710 720 730 740 750
VRTISALAIA ALAEAATPYG IESFDSVLKP LWKGIRQHRG KGLAAFLKAI
760 770 780 790 800
GYLIPLMDAE YANYYTREVM LILIREFQSP DEEMKKIVLK VVKQCCGTDG
810 820 830 840 850
VEANYIKTEI LPPFFKHFWQ HRMALDRRNY RQLVDTTVEL ANKVGAAEII
860 870 880 890 900
SRIVDDLKDE AEQYRKMVME TIEKIMGNLG AADIDHKLEE QLIDGILYAF
910 920 930 940 950
QEQTTEDSVM LNGFGTVVNA LGKRVKPYLP QICGTVLWRL NNKSAKVRQQ
960 970 980 990 1000
AADLISRTAV VMKTCQEEKL MGHLGVVLYE YLGEEYPEVL GSILGALKAI
1010 1020 1030 1040 1050
VNVIGMHKMT PPIKDLLPRL TPILKNRHEK VQENCIDLVG RIADRGAEYV
1060 1070 1080 1090 1100
SAREWMRICF ELLELLKAHK KAIRRATVNT FGYIAKAIGP HDVLATLLNN
1110 1120 1130 1140 1150
LKVQERQNRV CTTVAIAIVA ETCSPFTVLP ALMNEYRVPE LNVQNGVLKS
1160 1170 1180 1190 1200
LSFLFEYIGE MGKDYIYAVT PLLEDALMDR DLVHRQTASA VVQHMSLGVY
1210 1220 1230 1240 1250
GFGCEDSLNH LLNYVWPNVF ETSPHVIQAV MGALEGLRVA IGPCRMLQYC
1260 1270 1280 1290 1300
LQGLFHPARK VRDVYWKIYN SIYIGSQDAL IAHYPRIYND DKNTYIRYEL

DYIL
Length:1,304
Mass (Da):145,830
Last modified:November 24, 2009 - v3
Checksum:i12F051757D2B9DEE
GO
Isoform 2 (identifier: O75533-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-144: GKTPD → FYSAA
     145-1304: Missing.

Note: No experimental confirmation available.
Show »
Length:144
Mass (Da):16,020
Checksum:i006D4294E06AB51E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti149A → V in AAC97189 (PubMed:9585501).Curated1
Sequence conflicti594R → L in AAC97189 (PubMed:9585501).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046182140 – 144GKTPD → FYSAA in isoform 2. 1 Publication5
Alternative sequenceiVSP_046183145 – 1304Missing in isoform 2. 1 PublicationAdd BLAST1160

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF054284 mRNA. Translation: AAC97189.1.
AF086296 mRNA. No translation available.
AC010746 Genomic DNA. No translation available.
AF070540 mRNA. Translation: AAC28633.1.
CCDSiCCDS33356.1. [O75533-1]
CCDS46479.1. [O75533-2]
RefSeqiNP_036565.2. NM_012433.3. [O75533-1]
UniGeneiHs.632554.

Genome annotation databases

EnsembliENST00000335508; ENSP00000335321; ENSG00000115524. [O75533-1]
ENST00000409915; ENSP00000428820; ENSG00000115524. [O75533-2]
ENST00000414963; ENSP00000402997; ENSG00000115524. [O75533-2]
GeneIDi23451.
KEGGihsa:23451.
UCSCiuc002uue.4. human. [O75533-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSF3B1_HUMAN
AccessioniPrimary (citable) accession number: O75533
Secondary accession number(s): E9PCH3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 14, 2001
Last sequence update: November 24, 2009
Last modified: September 27, 2017
This is version 173 of the entry and version 3 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 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families