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Q15427 (SF3B4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 152. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length424 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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 complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42/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.13

Sequence similarities

Belongs to the SF3B4 family.

Contains 2 RRM (RNA recognition motif) domains.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5
Chain2 – 424423Splicing factor 3B subunit 4
PRO_0000081955

Regions

Domain13 – 9179RRM 1
Domain100 – 17980RRM 2
Compositional bias215 – 2184Poly-Pro
Compositional bias262 – 2687Poly-Pro

Amino acid modifications

Modified residue21N-acetylalanine Ref.5 Ref.11 Ref.14 Ref.15
Modified residue561Phosphotyrosine Ref.10

Secondary structure

............................... 424
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q15427 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 212472A25D3FF002

FASTA42444,386
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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. expand/collapse author list , 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, IDENTIFICATION BY 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, IDENTIFICATION BY 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, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"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] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"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].
[13]"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. expand/collapse author list , 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.
[14]"Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"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.
CCDSCCDS941.1.
PIRA54964.
RefSeqNP_005841.1. NM_005850.4.
XP_005277388.1. XM_005277331.2.
UniGeneHs.516160.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1X5TNMR-A102-184[»]
1X5UNMR-A5-96[»]
ProteinModelPortalQ15427.
SMRQ15427. Positions 5-186.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115554. 87 interactions.
IntActQ15427. 37 interactions.
MINTMINT-1032702.
STRING9606.ENSP00000271628.

PTM databases

PhosphoSiteQ15427.

Polymorphism databases

DMDM2500587.

Proteomic databases

MaxQBQ15427.
PaxDbQ15427.
PeptideAtlasQ15427.
PRIDEQ15427.

Protocols and materials databases

DNASU10262.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000271628; ENSP00000271628; ENSG00000143368.
ENST00000582851; ENSP00000462063; ENSG00000263977.
GeneID10262.
KEGGhsa:10262.
UCSCuc001etk.2. human.

Organism-specific databases

CTD10262.
GeneCardsGC01M149895.
HGNCHGNC:10771. SF3B4.
HPAHPA028578.
MIM154400. phenotype.
605593. gene.
neXtProtNX_Q15427.
Orphanet245. Nager syndrome.
PharmGKBPA35689.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0724.
HOGENOMHOG000200535.
HOVERGENHBG002295.
InParanoidQ15427.
KOK12831.
OMAAMVYEIM.
PhylomeDBQ15427.
TreeFamTF300890.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.

Gene expression databases

ArrayExpressQ15427.
BgeeQ15427.
CleanExHS_SF3B4.
GenevestigatorQ15427.

Family and domain databases

Gene3D3.30.70.330. 2 hits.
InterProIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTSM00360. RRM. 2 hits.
[Graphical view]
PROSITEPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ15427.
GeneWikiSF3B4.
GenomeRNAi10262.
NextBio38880.
PROQ15427.
SOURCESearch...

Entry information

Entry nameSF3B4_HUMAN
AccessionPrimary (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: July 9, 2014
This is version 152 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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

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

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM