Q15459 (SF3A1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Splicing factor 3A subunit 1

Alternative name(s):
SF3a120
Spliceosome-associated protein 114
Short name=SAP 114

Gene names

Name:	SF3A1
Synonyms:	SAP114

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	793 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Polymorphism
Domain	Repeat
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA 3'-splice site recognition Traceable author statement PubMed 15647371. Source: HGNC
Cellular_component	U2-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_function	RNA binding Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MAP1LC3C	Q9BXW4	3	EBI-1054743,EBI-2603996
SP1	P08047	2	EBI-1054743,EBI-298336

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 793

793

Splicing factor 3A subunit 1

PRO_0000114917

Regions

Repeat

52 – 94

43

SURP motif 1

Repeat

166 – 208

43

SURP motif 2

Domain

707 – 793

87

Ubiquitin-like

Compositional bias

10 – 16

7

Poly-Pro

Compositional bias

118 – 122

5

Poly-Gln

Compositional bias

260 – 267

8

Poly-Glu

Compositional bias

369 – 372

4

Poly-Pro

Compositional bias

557 – 560

4

Poly-Pro

Compositional bias

672 – 675

4

Poly-Pro

Sites

Site

169

1

Critical for binding to SF3A3

Amino acid modifications

Modified residue

55

1

N6-acetyllysine Ref.13

Modified residue

320

1

Phosphoserine Ref.12 Ref.16

Modified residue

329

1

Phosphoserine Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.14 Ref.16

Modified residue

359

1

Phosphoserine Ref.8 Ref.12 Ref.14 Ref.16

Modified residue

413

1

Phosphoserine Ref.10 Ref.14

Modified residue

451

1

Phosphoserine Ref.10 Ref.12 Ref.14

Modified residue

456

1

Phosphotyrosine Ref.7

Modified residue

759

1

Phosphotyrosine Ref.7

Natural variations

Natural variant

511

1

R → W in a colorectal cancer sample; somatic mutation. Ref.19

VAR_036290

Experimental info

Mutagenesis

48

1

E → F: SLURP 1 motif acquires binding to SF3A3; when associated to Leu-55. Ref.18

Mutagenesis

55

1

K → L: SLURP 1 motif acquires binding to SF3A3; when associated to Phe-48. Ref.18

Mutagenesis

162

1

F → E: No effect on binding to SF3A3. Ref.18

Mutagenesis

169

1

L → K: Abolishes binding to SF3A3. Ref.18

Secondary structure

1

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793

Helix Strand Turn

Details...

Helix

48 – 63

16

Helix

66 – 74

9

Helix

79 – 84

6

Helix

91 – 103

13

Helix

161 – 177

17

Helix

179 – 188

10

Turn

189 – 191

3

Helix

193 – 198

6

Helix

204 – 215

12

Beta strand

705 – 710

6

Beta strand

715 – 721

7

Beta strand

726 – 731

6

Helix

737 – 747

11

Turn

752 – 754

3

Beta strand

755 – 759

5

Beta strand

762 – 764

3

Helix

770 – 773

4

Beta strand

779 – 786

8

Sequences

	Sequence		Length	Mass (Da)
	Q15459 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 7259F1EC4577305C	FASTA	793	88,886
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.

IPI

IPI00017451.

PIR

S60735.

RefSeq

NP_001005409.1. NM_001005409.1.
NP_005868.1. NM_005877.4.

UniGene

Hs.406277.
Hs.505597.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZKH	NMR	-	A	704-789	[»]
2DT6	NMR	-	A	48-110	[»]
2DT7	NMR	-	B	134-217	[»]

ProteinModelPortal

Q15459.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29164N.

IntAct

Q15459. 14 interactions.

MINT

MINT-144269.

STRING

9606.ENSP00000215793.

PTM databases

PhosphoSite

Q15459.

Polymorphism databases

DMDM

2498882.

Proteomic databases

PaxDb

Q15459.

PeptideAtlas

Q15459.

PRIDE

Q15459.

Protocols and materials databases

DNASU

10291.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000215793; ENSP00000215793; ENSG00000099995.

GeneID

10291.

KEGG

hsa:10291.

UCSC

uc003ahl.3. human.

Organism-specific databases

CTD

10291.

GeneCards

GC22M030727.

HGNC

HGNC:10765. SF3A1.

HPA

HPA000690.
HPA030083.

MIM

605595. gene.

neXtProt

NX_Q15459.

PharmGKB

PA35683.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG300902.

HOGENOM

HOG000238941.

HOVERGEN

HBG059993.

InParanoid

Q15459.

KO

K12825.

OMA

GMPPAKQ.

OrthoDB

EOG4N5VWN.

PhylomeDB

Q15459.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q15459.

Bgee

Q15459.

CleanEx

HS_SF3A1.

Genevestigator

Q15459.

GermOnline

ENSG00000099995. Homo sapiens.

Family and domain databases

InterPro

IPR022030. PRP21-like.
IPR000061. Surp.
IPR000626. Ubiquitin.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF12230. PRP21_like_P. 1 hit.
PF01805. Surp. 2 hits.
PF00240. ubiquitin. 1 hit.
[Graphical view]

SMART

SM00648. SWAP. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]

SUPFAM

SSF109905. SSF109905. 2 hits.

PROSITE

PS50128. SURP. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

SF3A1. human.

EvolutionaryTrace

Q15459.

GenomeRNAi

10291.

NextBio

39000.

PMAP-CutDB

Q15459.

SOURCE

Search...

Entry information

Entry name

SF3A1_HUMAN

Accession

Primary (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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.