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Q15427

- SF3B4_HUMAN

UniProt

Q15427 - SF3B4_HUMAN

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Protein

Splicing factor 3B subunit 4

Gene
SF3B4, SAP49
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.

GO - Molecular functioni

  1. nucleotide binding Source: InterPro
  2. poly(A) RNA binding Source: UniProtKB
  3. protein binding Source: IntAct

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA processing Source: ProtInc
  3. mRNA splicing, via spliceosome Source: HGNC
  4. RNA splicing Source: Reactome
  5. RNA splicing, via transesterification reactions Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
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 namesi
Name:SF3B4
Synonyms:SAP49
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:10771. SF3B4.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleoplasm Source: Reactome
  2. spliceosomal complex Source: HGNC
  3. U12-type spliceosomal complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

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.1 Publication

Organism-specific databases

MIMi154400. phenotype.
Orphaneti245. Nager syndrome.
PharmGKBiPA35689.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 424423Splicing factor 3B subunit 4PRO_0000081955Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine4 Publications
Modified residuei56 – 561Phosphotyrosine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ15427.
PaxDbiQ15427.
PeptideAtlasiQ15427.
PRIDEiQ15427.

PTM databases

PhosphoSiteiQ15427.

Expressioni

Gene expression databases

ArrayExpressiQ15427.
BgeeiQ15427.
CleanExiHS_SF3B4.
GenevestigatoriQ15427.

Organism-specific databases

HPAiHPA028578.

Interactioni

Subunit structurei

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 SF3B2.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BCAS2O759342EBI-348469,EBI-1050106
EFTUD2Q150292EBI-348469,EBI-357897
GRB2P629932EBI-348469,EBI-401755
PRPF8Q6P2Q92EBI-348469,EBI-538479
RBM10P981752EBI-348469,EBI-721525
SF3B2Q134353EBI-348469,EBI-749111
WDR83Q9BRX92EBI-348469,EBI-7705033

Protein-protein interaction databases

BioGridi115554. 87 interactions.
IntActiQ15427. 37 interactions.
MINTiMINT-1032702.
STRINGi9606.ENSP00000271628.

Structurei

Secondary structure

1
424
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni11 – 133
Beta strandi14 – 185
Helixi26 – 349
Beta strandi39 – 435
Beta strandi48 – 503
Beta strandi57 – 637
Helixi64 – 7310
Beta strandi74 – 763
Beta strandi85 – 884
Turni89 – 924
Beta strandi102 – 1054
Helixi113 – 1219
Beta strandi126 – 1283
Turni136 – 1383
Beta strandi143 – 1519
Helixi152 – 1609
Turni161 – 1644
Beta strandi173 – 1775

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X5TNMR-A102-184[»]
1X5UNMR-A5-96[»]
ProteinModelPortaliQ15427.
SMRiQ15427. Positions 5-186.

Miscellaneous databases

EvolutionaryTraceiQ15427.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 9179RRM 1Add
BLAST
Domaini100 – 17980RRM 2Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi215 – 2184Poly-Pro
Compositional biasi262 – 2687Poly-Pro

Sequence similaritiesi

Belongs to the SF3B4 family.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0724.
HOGENOMiHOG000200535.
HOVERGENiHBG002295.
InParanoidiQ15427.
KOiK12831.
OMAiAMVYEIM.
PhylomeDBiQ15427.
TreeFamiTF300890.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q15427-1 [UniParc]FASTAAdd to Basket

« Hide

MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT    50
GQHQGYGFVE FLSEEDADYA IKIMNMIKLY GKPIRVNKAS AHNKNLDVGA 100
NIFIGNLDPE IDEKLLYDTF SAFGVILQTP KIMRDPDTGN SKGYAFINFA 150
SFDASDAAIE AMNGQYLCNR PITVSYAFKK DSKGERHGSA AERLLAAQNP 200
LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP GSFPPPVPPP 250
GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG 300
MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG 350
MPPRGPPFGS PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP 400
LPPPRPTPRP PVPPRGPLRG PLPQ 424
Length:424
Mass (Da):44,386
Last modified:November 1, 1996 - v1
Checksum:i212472A25D3FF002
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS941.1.
PIRiA54964.
RefSeqiNP_005841.1. NM_005850.4.
XP_005277388.1. XM_005277331.2.
UniGeneiHs.516160.

Genome annotation databases

EnsembliENST00000271628; ENSP00000271628; ENSG00000143368.
ENST00000582851; ENSP00000462063; ENSG00000263977.
GeneIDi10262.
KEGGihsa:10262.
UCSCiuc001etk.2. human.

Polymorphism databases

DMDMi2500587.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS941.1.
PIRi A54964.
RefSeqi NP_005841.1. NM_005850.4.
XP_005277388.1. XM_005277331.2.
UniGenei Hs.516160.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1X5T NMR - A 102-184 [» ]
1X5U NMR - A 5-96 [» ]
ProteinModelPortali Q15427.
SMRi Q15427. Positions 5-186.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 115554. 87 interactions.
IntActi Q15427. 37 interactions.
MINTi MINT-1032702.
STRINGi 9606.ENSP00000271628.

PTM databases

PhosphoSitei Q15427.

Polymorphism databases

DMDMi 2500587.

Proteomic databases

MaxQBi Q15427.
PaxDbi Q15427.
PeptideAtlasi Q15427.
PRIDEi Q15427.

Protocols and materials databases

DNASUi 10262.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000271628 ; ENSP00000271628 ; ENSG00000143368 .
ENST00000582851 ; ENSP00000462063 ; ENSG00000263977 .
GeneIDi 10262.
KEGGi hsa:10262.
UCSCi uc001etk.2. human.

Organism-specific databases

CTDi 10262.
GeneCardsi GC01M149895.
HGNCi HGNC:10771. SF3B4.
HPAi HPA028578.
MIMi 154400. phenotype.
605593. gene.
neXtProti NX_Q15427.
Orphaneti 245. Nager syndrome.
PharmGKBi PA35689.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0724.
HOGENOMi HOG000200535.
HOVERGENi HBG002295.
InParanoidi Q15427.
KOi K12831.
OMAi AMVYEIM.
PhylomeDBi Q15427.
TreeFami TF300890.

Enzyme and pathway databases

Reactomei REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Miscellaneous databases

EvolutionaryTracei Q15427.
GeneWikii SF3B4.
GenomeRNAii 10262.
NextBioi 38880.
PROi Q15427.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q15427.
Bgeei Q15427.
CleanExi HS_SF3B4.
Genevestigatori Q15427.

Family and domain databases

Gene3Di 3.30.70.330. 2 hits.
InterProi IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view ]
Pfami PF00076. RRM_1. 2 hits.
[Graphical view ]
SMARTi SM00360. RRM. 2 hits.
[Graphical view ]
PROSITEi PS50102. RRM. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. 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. 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.

Entry informationi

Entry nameiSF3B4_HUMAN
AccessioniPrimary (citable) accession number: Q15427
Secondary accession number(s): Q5SZ63
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: September 3, 2014
This is version 153 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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