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Protein

Splicing factor 3A subunit 1

Gene

SF3A1

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

  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA 3'-splice site recognition Source: HGNC
  • mRNA processing Source: HGNC
  • mRNA splicing, via spliceosome Source: UniProtKB

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000099995.18
HGNCiHGNC:10765 SF3A1
MIMi605595 gene
neXtProtiNX_Q15459

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
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
Cross-linki20Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei55N6-acetyllysineCombined sources1
Cross-linki131Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei320PhosphoserineCombined sources1
Modified residuei329PhosphoserineCombined sources1
Modified residuei359PhosphoserineCombined sources1
Modified residuei413PhosphoserineCombined sources1
Cross-linki424Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei451PhosphoserineCombined sources1
Modified residuei456PhosphotyrosineCombined sources1
Cross-linki499Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
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
ProteomicsDBi60599

PTM databases

iPTMnetiQ15459
PhosphoSitePlusiQ15459
SwissPalmiQ15459

Miscellaneous databases

PMAP-CutDBiQ15459

Expressioni

Tissue specificityi

Ubiquitously expressed.

Gene expression databases

BgeeiENSG00000099995 Expressed in 236 organ(s), highest expression level in testis
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

Protein-protein interaction databases

BioGridi115580, 232 interactors
CORUMiQ15459
DIPiDIP-29164N
IntActiQ15459, 39 interactors
MINTiQ15459
STRINGi9606.ENSP00000215793

Structurei

Secondary structure

1793
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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.

Keywords - Domaini

Repeat

Phylogenomic databases

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

Family and domain databases

CDDicd01800 SF3a120_C, 1 hit
Gene3Di1.10.10.790, 2 hits
InterProiView protein in InterPro
IPR022030 SF3A1
IPR035563 SF3As1_ubi
IPR000061 Surp
IPR035967 SWAP/Surp_sf
IPR029071 Ubiquitin-like_domsf
IPR000626 Ubiquitin_dom
PfamiView protein in Pfam
PF12230 PRP21_like_P, 1 hit
PF01805 Surp, 2 hits
PF00240 ubiquitin, 1 hit
SMARTiView protein in SMART
SM00648 SWAP, 2 hits
SM00213 UBQ, 1 hit
SUPFAMiSSF109905 SSF109905, 2 hits
SSF54236 SSF54236, 1 hit
PROSITEiView protein in PROSITE
PS50128 SURP, 2 hits
PS50053 UBIQUITIN_2, 1 hit

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

This entry has 2 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F8WB66F8WB66_HUMAN
Splicing factor 3A subunit 1
SF3A1
63Annotation score:
H7C1L2H7C1L2_HUMAN
Splicing factor 3A subunit 1
SF3A1
259Annotation score:
F8WC79F8WC79_HUMAN
Splicing factor 3A subunit 1
SF3A1
38Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_036290511R → W in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs765594577Ensembl.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

Similar proteinsi

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[»]
5Z56electron microscopy5.10u1-793[»]
5Z57electron microscopy6.50w310-384[»]
5Z58electron microscopy4.90w310-384[»]
ProteinModelPortaliQ15459
SMRiQ15459
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115580, 232 interactors
CORUMiQ15459
DIPiDIP-29164N
IntActiQ15459, 39 interactors
MINTiQ15459
STRINGi9606.ENSP00000215793

PTM databases

iPTMnetiQ15459
PhosphoSitePlusiQ15459
SwissPalmiQ15459

Polymorphism and mutation databases

BioMutaiSF3A1
DMDMi2498882

Proteomic databases

EPDiQ15459
MaxQBiQ15459
PaxDbiQ15459
PeptideAtlasiQ15459
PRIDEiQ15459
ProteomicsDBi60599

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
EuPathDBiHostDB:ENSG00000099995.18
GeneCardsiSF3A1
HGNCiHGNC:10765 SF3A1
HPAiHPA000690
HPA030083
MIMi605595 gene
neXtProtiNX_Q15459
OpenTargetsiENSG00000099995
PharmGKBiPA35683
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

ChiTaRSiSF3A1 human
EvolutionaryTraceiQ15459
GeneWikiiSF3A1
GenomeRNAii10291
PMAP-CutDBiQ15459
PROiPR:Q15459
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000099995 Expressed in 236 organ(s), highest expression level in testis
CleanExiHS_SF3A1
ExpressionAtlasiQ15459 baseline and differential
GenevisibleiQ15459 HS

Family and domain databases

CDDicd01800 SF3a120_C, 1 hit
Gene3Di1.10.10.790, 2 hits
InterProiView protein in InterPro
IPR022030 SF3A1
IPR035563 SF3As1_ubi
IPR000061 Surp
IPR035967 SWAP/Surp_sf
IPR029071 Ubiquitin-like_domsf
IPR000626 Ubiquitin_dom
PfamiView protein in Pfam
PF12230 PRP21_like_P, 1 hit
PF01805 Surp, 2 hits
PF00240 ubiquitin, 1 hit
SMARTiView protein in SMART
SM00648 SWAP, 2 hits
SM00213 UBQ, 1 hit
SUPFAMiSSF109905 SSF109905, 2 hits
SSF54236 SSF54236, 1 hit
PROSITEiView protein in PROSITE
PS50128 SURP, 2 hits
PS50053 UBIQUITIN_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSF3A1_HUMAN
AccessioniPrimary (citable) accession number: Q15459
Secondary accession number(s): E9PAW1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 7, 2018
This is version 195 of the entry and version 1 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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