Q15427 (SF3B4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Splicing factor 3B subunit 4

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

Gene names

Name:	SF3B4
Synonyms:	SAP49

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	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). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. SF3B4 interacts directly with SF3B2. Ref.7 Ref.8 Ref.9
Subcellular location	Nucleus By similarity.
Involvement in disease	Acrofacial dysostosis 1, Nager type (AFD1) [MIM:154400]: A form of acrofacial dysostosis, a group of disorders which are characterized by malformation of the craniofacial skeleton and the limbs. The major facial features of AFD1 include downslanted palpebral fissures, midface retrusion, and micrognathia, the latter of which often requires the placement of a tracheostomy in early childhood. Limb defects typically involve the anterior (radial) elements of the upper limbs and manifest as small or absent thumbs, triphalangeal thumbs, radial hyoplasia or aplasia, and radioulnar synostosis. Phocomelia of the upper limbs and, occasionally, lower-limb defects have also been reported. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.12
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 Reference proteome
Gene Ontology (GO)
Biological_process	mRNA splicing, via spliceosome Inferred by curator PubMed 9731529. Source: HGNC
Cellular_component	U12-type spliceosomal complex Inferred from direct assay Ref.9. Source: UniProtKB nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GRB2	P62993	2	EBI-348469,EBI-401755

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

56

1

Phosphotyrosine Ref.10

Secondary structure

1

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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 [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE SF3B COMPLEX, ELECTRON MICROSCOPY OF THE SF3B COMPLEX.
[9]	"The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome." Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R. RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, MASS SPECTROMETRY.
[10]	"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-56, MASS SPECTROMETRY.
[11]	"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].
[12]	"Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome." Bernier F.P., Caluseriu O., Ng S., Schwartzentruber J., Buckingham K.J., Innes A.M., Jabs E.W., Innis J.W., Schuette J.L., Gorski J.L., Byers P.H., Andelfinger G., Siu V., Lauzon J., Fernandez B.A., McMillin M., Scott R.H., Racher H. , Majewski J., Nickerson D.A., Shendure J., Bamshad M.J., Parboosingh J.S. Am. J. Hum. Genet. 90:925-933(2012) [PubMed] [Europe PMC] [Abstract] Cited for: INVOLVEMENT IN AFD1.
[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

EMBL
GenBank
DDBJ

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. NM_005850.4.

UniGene

Hs.516160.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

Q15427.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q15427. 15 interactions.

MINT

MINT-1032702.

STRING

9606.ENSP00000271628.

PTM databases

PhosphoSite

Q15427.

Polymorphism databases

DMDM

2500587.

Proteomic databases

PaxDb

Q15427.

PeptideAtlas

Q15427.

PRIDE

Q15427.

Protocols and materials databases

DNASU

10262.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000271628; ENSP00000271628; ENSG00000143368.
ENST00000582851; ENSP00000462063; ENSG00000263977.

GeneID

10262.

KEGG

hsa:10262.

UCSC

uc001etk.2. human.

Organism-specific databases

CTD

10262.

GeneCards

GC01M149895.

HGNC

HGNC:10771. SF3B4.

HPA

HPA028578.

MIM

154400. phenotype.
605593. gene.

neXtProt

NX_Q15427.

Orphanet

245. Acrofacial dysostosis, Nager type.

PharmGKB

PA35689.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0724.

HOGENOM

HOG000200535.

HOVERGEN

HBG002295.

InParanoid

Q15427.

KO

K12831.

OMA

VSETLLW.

OrthoDB

EOG4M65JJ.

PhylomeDB

Q15427.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q15427.

Bgee

Q15427.

CleanEx

HS_SF3B4.

Genevestigator

Q15427.

GermOnline

ENSG00000143368. Homo sapiens.

Family and domain databases

Gene3D

3.30.70.330. 2 hits.

InterPro

IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]

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

EvolutionaryTrace

Q15427.

GenomeRNAi

10262.

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:	May 1, 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.