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Protein

Splicing factor 3A subunit 1

Gene

SF3A1

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 SF3A 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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei169Critical for binding to SF3A31

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA 3'-splice site recognition Source: HGNC
  • mRNA processing Source: HGNC
  • mRNA splicing, via spliceosome Source: UniProtKB
  • regulation of alternative mRNA splicing, via spliceosome Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciZFISH:ENSG00000099995-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor 3A subunit 1
Alternative name(s):
SF3a120
Spliceosome-associated protein 114
Short name:
SAP 114
Gene namesi
Name:SF3A1
Synonyms:SAP114
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

HGNCiHGNC:10765. SF3A1.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • nucleoplasm Source: HPA
  • spliceosomal complex Source: HGNC
  • U2 snRNP Source: GO_Central
  • U2-type prespliceosome Source: GO_Central
  • U2-type spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi48E → F: SLURP 1 motif acquires binding to SF3A3; when associated with Leu-55. 1 Publication1
Mutagenesisi55K → L: SLURP 1 motif acquires binding to SF3A3; when associated with Phe-48. 1 Publication1
Mutagenesisi162F → E: No effect on binding to SF3A3. 1 Publication1
Mutagenesisi169L → K: Abolishes binding to SF3A3. 1 Publication1

Organism-specific databases

DisGeNETi10291.
OpenTargetsiENSG00000099995.
PharmGKBiPA35683.

Polymorphism and mutation databases

BioMutaiSF3A1.
DMDMi2498882.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001149172 – 793Splicing factor 3A subunit 1Add BLAST792

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei55N6-acetyllysineCombined sources1
Modified residuei320PhosphoserineCombined sources1
Modified residuei329PhosphoserineCombined sources1
Modified residuei359PhosphoserineCombined sources1
Modified residuei413PhosphoserineCombined sources1
Modified residuei451PhosphoserineCombined sources1
Modified residuei456PhosphotyrosineCombined sources1
Modified residuei508PhosphoserineCombined sources1
Cross-linki542Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki686Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei759PhosphotyrosineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ15459.
MaxQBiQ15459.
PaxDbiQ15459.
PeptideAtlasiQ15459.
PRIDEiQ15459.

PTM databases

iPTMnetiQ15459.
PhosphoSitePlusiQ15459.
SwissPalmiQ15459.

Miscellaneous databases

PMAP-CutDBQ15459.

Expressioni

Tissue specificityi

Ubiquitously expressed.

Gene expression databases

BgeeiENSG00000099995.
CleanExiHS_SF3A1.
ExpressionAtlasiQ15459. baseline and differential.
GenevisibleiQ15459. HS.

Organism-specific databases

HPAiHPA000690.
HPA030083.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. Component of splicing factor SF3A which is composed of three subunits; SF3A3/SAP61, SF3A2/SAP62, SF3A1/SAP114. SF3A associates with the splicing factor SF3B and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Interacts with SF3A3.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
MAP1LC3CQ9BXW43EBI-1054743,EBI-2603996
PRPF40AO754002EBI-1054743,EBI-473291
RBM10P981752EBI-1054743,EBI-721525
SF1Q156378EBI-1054743,EBI-744603
SF3A2Q154283EBI-1054743,EBI-2462271
SF3A3Q128742EBI-1054743,EBI-1051880
SP1P080472EBI-1054743,EBI-298336

Protein-protein interaction databases

BioGridi115580. 174 interactors.
DIPiDIP-29164N.
IntActiQ15459. 36 interactors.
MINTiMINT-144269.
STRINGi9606.ENSP00000215793.

Structurei

Secondary structure

1793
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi48 – 63Combined sources16
Helixi66 – 74Combined sources9
Helixi79 – 84Combined sources6
Helixi91 – 103Combined sources13
Helixi161 – 177Combined sources17
Helixi179 – 188Combined sources10
Turni189 – 191Combined sources3
Helixi193 – 198Combined sources6
Helixi204 – 215Combined sources12
Beta strandi705 – 710Combined sources6
Beta strandi715 – 721Combined sources7
Beta strandi726 – 731Combined sources6
Helixi737 – 747Combined sources11
Turni752 – 754Combined sources3
Beta strandi755 – 759Combined sources5
Beta strandi762 – 764Combined sources3
Helixi770 – 773Combined sources4
Beta strandi779 – 786Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZKHNMR-A704-789[»]
2DT6NMR-A48-110[»]
2DT7NMR-B134-217[»]
ProteinModelPortaliQ15459.
SMRiQ15459.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ15459.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati52 – 94SURP motif 1Add BLAST43
Repeati166 – 208SURP motif 2Add BLAST43
Domaini707 – 793Ubiquitin-likePROSITE-ProRule annotationAdd BLAST87

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 16Poly-Pro7
Compositional biasi118 – 122Poly-Gln5
Compositional biasi260 – 267Poly-Glu8
Compositional biasi369 – 372Poly-Pro4
Compositional biasi557 – 560Poly-Pro4
Compositional biasi672 – 675Poly-Pro4

Domaini

SURP motif 2 mediates direct binding to SF3A3.

Sequence similaritiesi

Contains 2 SURP motif repeats.PROSITE-ProRule annotation
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0007. Eukaryota.
ENOG410XPNW. LUCA.
GeneTreeiENSGT00730000111077.
HOGENOMiHOG000238941.
HOVERGENiHBG059993.
InParanoidiQ15459.
KOiK12825.
OMAiNEMPQPP.
OrthoDBiEOG091G0539.
PhylomeDBiQ15459.
TreeFamiTF105705.

Family and domain databases

InterProiIPR022030. SF3A1.
IPR000061. Surp.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF12230. PRP21_like_P. 1 hit.
PF01805. Surp. 2 hits.
PF00240. ubiquitin. 1 hit.
[Graphical view]
SMARTiSM00648. SWAP. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF109905. SSF109905. 2 hits.
SSF54236. SSF54236. 1 hit.
PROSITEiPS50128. SURP. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform 1 (identifier: Q15459-1) [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
MPAGPVQAVP PPPPVPTEPK QPTEEEASSK EDSAPSKPVV GIIYPPPEVR
60 70 80 90 100
NIVDKTASFV ARNGPEFEAR IRQNEINNPK FNFLNPNDPY HAYYRHKVSE
110 120 130 140 150
FKEGKAQEPS AAIPKVMQQQ QQTTQQQLPQ KVQAQVIQET IVPKEPPPEF
160 170 180 190 200
EFIADPPSIS AFDLDVVKLT AQFVARNGRQ FLTQLMQKEQ RNYQFDFLRP
210 220 230 240 250
QHSLFNYFTK LVEQYTKILI PPKGLFSKLK KEAENPREVL DQVCYRVEWA
260 270 280 290 300
KFQERERKKE EEEKEKERVA YAQIDWHDFV VVETVDFQPN EQGNFPPPTT
310 320 330 340 350
PEELGARILI QERYEKFGES EEVEMEVESD EEDDKQEKAE EPPSQLDQDT
360 370 380 390 400
QVQDMDEGSD DEEEGQKVPP PPETPMPPPL PPTPDQVIVR KDYDPKASKP
410 420 430 440 450
LPPAPAPDEY LVSPITGEKI PASKMQEHMR IGLLDPRWLE QRDRSIREKQ
460 470 480 490 500
SDDEVYAPGL DIESSLKQLA ERRTDIFGVE ETAIGKKIGE EEIQKPEEKV
510 520 530 540 550
TWDGHSGSMA RTQQAAQANI TLQEQIEAIH KAKGLVPEDD TKEKIGPSKP
560 570 580 590 600
NEIPQQPPPP SSATNIPSSA PPITSVPRPP TMPPPVRTTV VSAVPVMPRP
610 620 630 640 650
PMASVVRLPP GSVIAPMPPI IHAPRINVVP MPPSAPPIMA PRPPPMIVPT
660 670 680 690 700
AFVPAPPVAP VPAPAPMPPV HPPPPMEDEP TSKKLKTEDS LMPEEEFLRR
710 720 730 740 750
NKGPVSIKVQ VPNMQDKTEW KLNGQVLVFT LPLTDQVSVI KVKIHEATGM
760 770 780 790
PAGKQKLQYE GIFIKDSNSL AYYNMANGAV IHLALKERGG RKK
Length:793
Mass (Da):88,886
Last modified:November 1, 1996 - v1
Checksum:i7259F1EC4577305C
GO
Isoform 2 (identifier: Q15459-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     106-170: Missing.

Note: No experimental confirmation available. Gene prediction based on EST data.
Show »
Length:728
Mass (Da):81,678
Checksum:i53E0FCDFB1CB4616
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_036290511R → W in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant rs765594577dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_054090106 – 170Missing in isoform 2. CuratedAdd BLAST65

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85237 mRNA. Translation: CAA59494.1.
CR456575 mRNA. Translation: CAG30461.1.
AC004997 Genomic DNA. Translation: AAC23435.1.
BC001976 mRNA. Translation: AAH01976.1.
BC007684 mRNA. Translation: AAH07684.1.
CCDSiCCDS13875.1. [Q15459-1]
PIRiS60735.
RefSeqiNP_005868.1. NM_005877.5. [Q15459-1]
UniGeneiHs.406277.
Hs.505597.

Genome annotation databases

EnsembliENST00000215793; ENSP00000215793; ENSG00000099995. [Q15459-1]
GeneIDi10291.
KEGGihsa:10291.
UCSCiuc003ahl.4. human. [Q15459-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85237 mRNA. Translation: CAA59494.1.
CR456575 mRNA. Translation: CAG30461.1.
AC004997 Genomic DNA. Translation: AAC23435.1.
BC001976 mRNA. Translation: AAH01976.1.
BC007684 mRNA. Translation: AAH07684.1.
CCDSiCCDS13875.1. [Q15459-1]
PIRiS60735.
RefSeqiNP_005868.1. NM_005877.5. [Q15459-1]
UniGeneiHs.406277.
Hs.505597.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZKHNMR-A704-789[»]
2DT6NMR-A48-110[»]
2DT7NMR-B134-217[»]
ProteinModelPortaliQ15459.
SMRiQ15459.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115580. 174 interactors.
DIPiDIP-29164N.
IntActiQ15459. 36 interactors.
MINTiMINT-144269.
STRINGi9606.ENSP00000215793.

PTM databases

iPTMnetiQ15459.
PhosphoSitePlusiQ15459.
SwissPalmiQ15459.

Polymorphism and mutation databases

BioMutaiSF3A1.
DMDMi2498882.

Proteomic databases

EPDiQ15459.
MaxQBiQ15459.
PaxDbiQ15459.
PeptideAtlasiQ15459.
PRIDEiQ15459.

Protocols and materials databases

DNASUi10291.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000215793; ENSP00000215793; ENSG00000099995. [Q15459-1]
GeneIDi10291.
KEGGihsa:10291.
UCSCiuc003ahl.4. human. [Q15459-1]

Organism-specific databases

CTDi10291.
DisGeNETi10291.
GeneCardsiSF3A1.
HGNCiHGNC:10765. SF3A1.
HPAiHPA000690.
HPA030083.
MIMi605595. gene.
neXtProtiNX_Q15459.
OpenTargetsiENSG00000099995.
PharmGKBiPA35683.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0007. Eukaryota.
ENOG410XPNW. LUCA.
GeneTreeiENSGT00730000111077.
HOGENOMiHOG000238941.
HOVERGENiHBG059993.
InParanoidiQ15459.
KOiK12825.
OMAiNEMPQPP.
OrthoDBiEOG091G0539.
PhylomeDBiQ15459.
TreeFamiTF105705.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000099995-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiSF3A1. human.
EvolutionaryTraceiQ15459.
GeneWikiiSF3A1.
GenomeRNAii10291.
PMAP-CutDBQ15459.
PROiQ15459.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000099995.
CleanExiHS_SF3A1.
ExpressionAtlasiQ15459. baseline and differential.
GenevisibleiQ15459. HS.

Family and domain databases

InterProiIPR022030. SF3A1.
IPR000061. Surp.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF12230. PRP21_like_P. 1 hit.
PF01805. Surp. 2 hits.
PF00240. ubiquitin. 1 hit.
[Graphical view]
SMARTiSM00648. SWAP. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF109905. SSF109905. 2 hits.
SSF54236. SSF54236. 1 hit.
PROSITEiPS50128. SURP. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSF3A1_HUMAN
AccessioniPrimary (citable) accession number: Q15459
Secondary accession number(s): E9PAW1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 178 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: 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.