Reviewed, UniProtKB/Swiss-Prot Q15427 (SF3B4_HUMAN)

Names and origin

Protein names

Recommended name:
    Splicing factor 3B subunit 4
Alternative name(s):
    Spliceosome-associated protein 49
      Short name=SAP 49
    SF3b50
    Pre-mRNA-splicing factor SF3b 49 kDa subunit

Gene names

Name:	SF3B4
Synonyms:	SAP49

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	424 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.
Subunit structure	Component of splicing factor SF3B which is composed of at least eight subunits; SF3B1/SAP155/SF3B155, SF3B2/SAP145/SF3B145, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B14A, PHF5A/SF3B14B, SF3B10 and SF3B125. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). SF3B4 interacts directly with SF3B2.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the SF3B4 family. Contains 2 RRM (RNA recognition motif) domains.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Repeat
Ligand	RNA-binding
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Uncategorized	? Ref.1 Traceable author statement. Source: ProtInc
Biological process	nuclear mRNA splicing, via spliceosome Inferred by curator. Source: HGNC
Cellular component	spliceosomal complex Ref.1 Inferred from direct assay. Source: HGNC
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ABL1	P00519	1	EBI-348469,EBI-375543
FYN	P06241	1	EBI-348469,EBI-515315
GRB2	P62993	1	EBI-348469,EBI-401755
NCK1	P16333	1	EBI-348469,EBI-389883
SMNDC1	O75940	1	EBI-348469,EBI-1052641
STK19	P49842	1	EBI-348469,EBI-347581

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 424

423

Splicing factor 3B subunit 4

PRO_0000081955

Regions

Domain

13 – 91

79

RRM 1

Domain

100 – 179

80

RRM 2

Compositional bias

215 – 218

4

Poly-Pro

Compositional bias

262 – 268

7

Poly-Pro

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.5

Modified residue

16

1

Phosphotyrosine Ref.10

Modified residue

56

1

Phosphotyrosine Ref.9

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

424

Helix Strand Turn

Details...

Turn

11 – 13

3

Beta strand

14 – 18

5

Helix

26 – 34

9

Beta strand

39 – 43

5

Beta strand

48 – 50

3

Beta strand

57 – 63

7

Helix

64 – 73

10

Beta strand

74 – 76

3

Beta strand

85 – 88

4

Turn

89 – 92

4

Beta strand

102 – 105

4

Helix

113 – 121

9

Beta strand

126 – 128

3

Turn

136 – 138

3

Beta strand

143 – 151

9

Helix

152 – 160

9

Turn

161 – 164

4

Beta strand

173 – 177

5

Sequences

	Sequence		Length	Mass (Da)
	Q15427-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 212472A25D3FF002	FASTA	424	44,386
	10 20 30 40 50 60 MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT GQHQGYGFVE 70 80 90 100 110 120 FLSEEDADYA IKIMNMIKLY GKPIRVNKAS AHNKNLDVGA NIFIGNLDPE IDEKLLYDTF 130 140 150 160 170 180 SAFGVILQTP KIMRDPDTGN SKGYAFINFA SFDASDAAIE AMNGQYLCNR PITVSYAFKK 190 200 210 220 230 240 DSKGERHGSA AERLLAAQNP LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP 250 260 270 280 290 300 GSFPPPVPPP GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG 310 320 330 340 350 360 MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG MPPRGPPFGS 370 380 390 400 410 420 PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP LPPPRPTPRP PVPPRGPLRG PLPQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The prespliceosome components SAP 49 and SAP 145 interact in a complex implicated in tethering U2 snRNP to the branch site." Champion-Arnaud P., Reed R. Genes Dev. 8:1974-1983(1994) [PubMed: 7958871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases 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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin and Testis.
[5]	Bienvenut W.V., Lilla S., von Kriegsheim A., Lempens A., Kolch W. Submitted (DEC-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-23, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY. Tissue: Ovarian carcinoma.
[6]	"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: 10882114] [Abstract] Cited for: CHARACTERIZATION OF THE SPLICEOSOME.
[7]	"Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein." Will C.L., Urlaub H., Achsel T., Gentzel M., Wilm M., Luehrmann R. EMBO J. 21:4978-4988(2002) [PubMed: 12234937] [Abstract] Cited for: IDENTIFICATION IN THE SF3B COMPLEX.
[8]	"Molecular architecture of the multiprotein splicing factor SF3b." Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H. Science 300:980-984(2003) [PubMed: 12738865] [Abstract] Cited for: IDENTIFICATION IN THE SF3B COMPLEX, ELECTRON MICROSCOPY OF THE SF3B COMPLEX.
[9]	"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: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-56, MASS SPECTROMETRY.
[10]	"Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer." Rikova K., Guo A., Zeng Q., Possemato A., Yu J., Haack H., Nardone J., Lee K., Reeves C., Li Y., Hu Y., Tan Z., Stokes M., Sullivan L., Mitchell J., Wetzel R., Macneill J., Ren J.M. , Yuan J., Bakalarski C.E., Villen J., Kornhauser J.M., Smith B., Li D., Zhou X., Gygi S.P., Gu T.-L., Polakiewicz R.D., Rush J., Comb M.J. Cell 131:1190-1203(2007) [PubMed: 18083107] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-16, MASS SPECTROMETRY.
[11]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[12]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY.
[13]	"Solution structure of RRM domains in splicing factor 3B." RIKEN structural genomics initiative (RSGI) Submitted (NOV-2005) to the PDB data bank Cited for: STRUCTURE BY NMR OF 4-184.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

L35013 Genomic DNA. Translation: AAA60300.1.
AL591493, AL590487 Genomic DNA. Translation: CAI12554.1.
AL590487, AL591493 Genomic DNA. Translation: CAI12648.1.
CH471121 Genomic DNA. Translation: EAW53595.1.
BC004273 mRNA. Translation: AAH04273.1.
BC013886 mRNA. Translation: AAH13886.1.
BC090883 mRNA. Translation: AAH90883.1.

IPI

IPI00017339.

PIR

A54964.

RefSeq

NP_005841.1.

UniGene

Hs.516160

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1X5T	NMR	-	A	102-184	[»]
1X5U	NMR	-	A	5-96	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q15427. 11 interactions.

STRING

Q15427.

PTM databases

PhosphoSite

Q15427.

Proteomic databases

PeptideAtlas

Q15427.

PRIDE

Q15427.

Genome annotation databases

Ensembl

ENST00000271628; ENSP00000271628; ENSG00000143368; Homo sapiens. [Genome view]

GeneID

10262.

KEGG

hsa:10262.

UCSC

uc001etj.1. human.

Organism-specific databases

CTD

10262.

GeneCards

GC01M148161.

H-InvDB

HIX0001007.

HGNC

HGNC:10771. SF3B4.

MIM

605593. gene.

PharmGKB

PA35689.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q15427.

HOVERGEN

Q15427.

OMA

MGMPPRA

OrthoDB

EOG998XKQ

Enzyme and pathway databases

Reactome

REACT_125. Processing of Capped Intron-Containing Pre-mRNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q15427.

Bgee

Q15427.

CleanEx

HS_SF3B4.

Genevestigator

Q15427.

GermOnline

ENSG00000143368. Homo sapiens.

Family and domain databases

InterPro

IPR012677. a_b_plait_nuc_bd.
IPR000504. RRM_RNP1.
[Graphical view]

Gene3D

G3DSA:3.30.70.330. a_b_plait_nuc_bd. 2 hits.

Pfam

PF00076. RRM_1. 2 hits.
[Graphical view]

SMART

SM00360. RRM. 2 hits.
[Graphical view]

PROSITE

PS50102. RRM. 2 hits.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

38880.

SOURCE

Search...

Entry information

Entry name

SF3B4_HUMAN

Accession

Primary (citable) accession number: Q15427
Secondary accession number(s): Q5SZ63

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	November 24, 2009
This is version 103 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.