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Q15459 (SF3A1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 140. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Splicing factor 3A subunit 1
Alternative name(s):
SF3a120
Spliceosome-associated protein 114
Short name=SAP 114
Gene names
Name:SF3A1
Synonyms:SAP114
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length793 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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. Ref.6 Ref.18

Subcellular location

Nucleus By similarity.

Tissue specificity

Ubiquitously expressed.

Domain

SURP motif 2 mediates direct binding to SF3A3.

Sequence similarities

Contains 2 SURP motif repeats.

Contains 1 ubiquitin-like domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentNucleus
Spliceosome
   Coding sequence diversityPolymorphism
   DomainRepeat
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processmRNA 3'-splice site recognition

Traceable author statement PubMed 15647371. Source: HGNC

   Cellular_componentU2-type spliceosomal complex

Inferred from direct assay Ref.5. Source: UniProtKB

catalytic step 2 spliceosome

Inferred from direct assay Ref.6. Source: UniProtKB

nucleoplasm

Traceable author statement. Source: Reactome

   Molecular_functionRNA binding

Inferred from direct assay Ref.5. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MAP1LC3CQ9BXW43EBI-1054743,EBI-2603996
SP1P080472EBI-1054743,EBI-298336

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 793793Splicing factor 3A subunit 1
PRO_0000114917

Regions

Repeat52 – 9443SURP motif 1
Repeat166 – 20843SURP motif 2
Domain707 – 79387Ubiquitin-like
Compositional bias10 – 167Poly-Pro
Compositional bias118 – 1225Poly-Gln
Compositional bias260 – 2678Poly-Glu
Compositional bias369 – 3724Poly-Pro
Compositional bias557 – 5604Poly-Pro
Compositional bias672 – 6754Poly-Pro

Sites

Site1691Critical for binding to SF3A3

Amino acid modifications

Modified residue551N6-acetyllysine Ref.13
Modified residue3201Phosphoserine Ref.12 Ref.16
Modified residue3291Phosphoserine Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.14 Ref.16
Modified residue3591Phosphoserine Ref.8 Ref.12 Ref.14 Ref.16
Modified residue4131Phosphoserine Ref.10 Ref.14
Modified residue4511Phosphoserine Ref.10 Ref.12 Ref.14
Modified residue4561Phosphotyrosine Ref.7
Modified residue7591Phosphotyrosine Ref.7

Natural variations

Natural variant5111R → W in a colorectal cancer sample; somatic mutation. Ref.19
VAR_036290

Experimental info

Mutagenesis481E → F: SLURP 1 motif acquires binding to SF3A3; when associated to Leu-55. Ref.18
Mutagenesis551K → L: SLURP 1 motif acquires binding to SF3A3; when associated to Phe-48. Ref.18
Mutagenesis1621F → E: No effect on binding to SF3A3. Ref.18
Mutagenesis1691L → K: Abolishes binding to SF3A3. Ref.18

Secondary structure

................................... 793
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q15459 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 7259F1EC4577305C

FASTA79388,886
        10         20         30         40         50         60 
MPAGPVQAVP PPPPVPTEPK QPTEEEASSK EDSAPSKPVV GIIYPPPEVR NIVDKTASFV 

        70         80         90        100        110        120 
ARNGPEFEAR IRQNEINNPK FNFLNPNDPY HAYYRHKVSE FKEGKAQEPS AAIPKVMQQQ 

       130        140        150        160        170        180 
QQTTQQQLPQ KVQAQVIQET IVPKEPPPEF EFIADPPSIS AFDLDVVKLT AQFVARNGRQ 

       190        200        210        220        230        240 
FLTQLMQKEQ RNYQFDFLRP QHSLFNYFTK LVEQYTKILI PPKGLFSKLK KEAENPREVL 

       250        260        270        280        290        300 
DQVCYRVEWA KFQERERKKE EEEKEKERVA YAQIDWHDFV VVETVDFQPN EQGNFPPPTT 

       310        320        330        340        350        360 
PEELGARILI QERYEKFGES EEVEMEVESD EEDDKQEKAE EPPSQLDQDT QVQDMDEGSD 

       370        380        390        400        410        420 
DEEEGQKVPP PPETPMPPPL PPTPDQVIVR KDYDPKASKP LPPAPAPDEY LVSPITGEKI 

       430        440        450        460        470        480 
PASKMQEHMR IGLLDPRWLE QRDRSIREKQ SDDEVYAPGL DIESSLKQLA ERRTDIFGVE 

       490        500        510        520        530        540 
ETAIGKKIGE EEIQKPEEKV TWDGHSGSMA RTQQAAQANI TLQEQIEAIH KAKGLVPEDD 

       550        560        570        580        590        600 
TKEKIGPSKP NEIPQQPPPP SSATNIPSSA PPITSVPRPP TMPPPVRTTV VSAVPVMPRP 

       610        620        630        640        650        660 
PMASVVRLPP GSVIAPMPPI IHAPRINVVP MPPSAPPIMA PRPPPMIVPT AFVPAPPVAP 

       670        680        690        700        710        720 
VPAPAPMPPV HPPPPMEDEP TSKKLKTEDS LMPEEEFLRR NKGPVSIKVQ VPNMQDKTEW 

       730        740        750        760        770        780 
KLNGQVLVFT LPLTDQVSVI KVKIHEATGM PAGKQKLQYE GIFIKDSNSL AYYNMANGAV 

       790 
IHLALKERGG RKK 

« Hide

References

« Hide 'large scale' references
[1]"Mammalian splicing factor SF3a120 represents a new member of the SURP family of proteins and is homologous to the essential splicing factor PRP21p of Saccharomyces cerevisiae."
Kraemer A., Mulhauser F., Wersig C., Groning K., Bilbe G.
RNA 1:260-272(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"A genome annotation-driven approach to cloning the human ORFeome."
Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I.
Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]"The DNA sequence of human chromosome 22."
Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. expand/collapse author list , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H.
Nature 402:489-495(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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].
Tissue: Cervix and Lymph.
[5]"Functional association of U2 snRNP with the ATP-independent spliceosomal complex E."
Das R., Zhou Z., Reed R.
Mol. Cell 5:779-787(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF THE SPLICEOSOME.
[6]"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.
[7]"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells."
Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J.
Nat. Biotechnol. 23:94-101(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-456 AND TYR-759, MASS SPECTROMETRY.
[8]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-329 AND SER-359, MASS SPECTROMETRY.
Tissue: Cervix carcinoma.
[9]"Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment."
Carrascal M., Ovelleiro D., Casas V., Gay M., Abian J.
J. Proteome Res. 7:5167-5176(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-329, MASS SPECTROMETRY.
Tissue: T-cell.
[10]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-329; SER-413 AND SER-451, MASS SPECTROMETRY.
Tissue: Cervix carcinoma.
[11]"Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography."
Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D., Zou H., Gu J.
Proteomics 8:1346-1361(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-329, MASS SPECTROMETRY.
Tissue: Liver.
[12]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-320; SER-329; SER-359 AND SER-451, MASS SPECTROMETRY.
Tissue: Leukemic T-cell.
[13]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-55, MASS SPECTROMETRY.
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-329; SER-359; SER-413 AND SER-451, MASS SPECTROMETRY.
Tissue: Cervix carcinoma.
[15]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-320; SER-329 AND SER-359, MASS SPECTROMETRY.
[17]"Solution structure of a human ubiquitin-like domain in SF3A1."
Structural genomics consortium (SGC)
Submitted (JUN-2005) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 704-789.
[18]"Solution structures of the SURP domains and the subunit-assembly mechanism within the splicing factor SF3a complex in 17S U2 snRNP."
Kuwasako K., He F., Inoue M., Tanaka A., Sugano S., Guntert P., Muto Y., Yokoyama S.
Structure 14:1677-1689(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 48-110 AND 134-217 IN COMPLEX WITH SF3A3, SUBUNIT, SURP MOTIFS, MUTAGENESIS OF GLU-48; LYS-55; PHE-162 AND LEU-169.
[19]"The consensus coding sequences of human breast and colorectal cancers."
Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. expand/collapse author list , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E.
Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT [LARGE SCALE ANALYSIS] TRP-511.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
IPIIPI00017451.
PIRS60735.
RefSeqNP_001005409.1. NM_001005409.1.
NP_005868.1. NM_005877.4.
UniGeneHs.406277.
Hs.505597.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZKHNMR-A704-789[»]
2DT6NMR-A48-110[»]
2DT7NMR-B134-217[»]
ProteinModelPortalQ15459.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-29164N.
IntActQ15459. 14 interactions.
MINTMINT-144269.
STRING9606.ENSP00000215793.

PTM databases

PhosphoSiteQ15459.

Polymorphism databases

DMDM2498882.

Proteomic databases

PaxDbQ15459.
PeptideAtlasQ15459.
PRIDEQ15459.

Protocols and materials databases

DNASU10291.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000215793; ENSP00000215793; ENSG00000099995.
GeneID10291.
KEGGhsa:10291.
UCSCuc003ahl.3. human.

Organism-specific databases

CTD10291.
GeneCardsGC22M030727.
HGNCHGNC:10765. SF3A1.
HPAHPA000690.
HPA030083.
MIM605595. gene.
neXtProtNX_Q15459.
PharmGKBPA35683.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG300902.
HOGENOMHOG000238941.
HOVERGENHBG059993.
InParanoidQ15459.
KOK12825.
OMAGMPPAKQ.
OrthoDBEOG4N5VWN.
PhylomeDBQ15459.

Enzyme and pathway databases

ReactomeREACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ15459.
BgeeQ15459.
CleanExHS_SF3A1.
GenevestigatorQ15459.
GermOnlineENSG00000099995. Homo sapiens.

Family and domain databases

InterProIPR022030. PRP21-like.
IPR000061. Surp.
IPR000626. Ubiquitin.
IPR019955. Ubiquitin_supergroup.
[Graphical view]
PfamPF12230. PRP21_like_P. 1 hit.
PF01805. Surp. 2 hits.
PF00240. ubiquitin. 1 hit.
[Graphical view]
SMARTSM00648. SWAP. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMSSF109905. SSF109905. 2 hits.
PROSITEPS50128. SURP. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSF3A1. human.
EvolutionaryTraceQ15459.
GenomeRNAi10291.
NextBio39000.
PMAP-CutDBQ15459.
SOURCESearch...

Entry information

Entry nameSF3A1_HUMAN
AccessionPrimary (citable) accession number: Q15459
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 29, 2013
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families