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Protein

Splicing factor 3B subunit 4

Gene

SF3B4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA processing Source: ProtInc
  3. mRNA splicing, via spliceosome Source: HGNC
  4. positive regulation of mRNA splicing, via spliceosome Source: Ensembl
  5. RNA splicing Source: Reactome
  6. 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 type1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:154400

Organism-specific databases

MIMi154400. phenotype.
Orphaneti245. Nager syndrome.
PharmGKBiPA35689.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed4 Publications
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

BgeeiQ15427.
CleanExiHS_SF3B4.
ExpressionAtlasiQ15427. baseline and differential.
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. 103 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 – 133Combined sources
Beta strandi14 – 185Combined sources
Helixi26 – 349Combined sources
Beta strandi39 – 435Combined sources
Beta strandi48 – 503Combined sources
Beta strandi57 – 637Combined sources
Helixi64 – 7310Combined sources
Beta strandi74 – 763Combined sources
Beta strandi85 – 884Combined sources
Turni89 – 924Combined sources
Beta strandi102 – 1054Combined sources
Helixi113 – 1219Combined sources
Beta strandi126 – 1283Combined sources
Turni136 – 1383Combined sources
Beta strandi143 – 1519Combined sources
Helixi152 – 1609Combined sources
Turni161 – 1644Combined sources
Beta strandi173 – 1775Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X5TNMR-A102-184[»]
1X5UNMR-A5-96[»]
ProteinModelPortaliQ15427.
SMRiQ15427. Positions 5-199.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ15427.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 9179RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini100 – 17980RRM 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

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

Sequence similaritiesi

Belongs to the SF3B4 family.Curated
Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0724.
GeneTreeiENSGT00760000119302.
HOGENOMiHOG000200535.
HOVERGENiHBG002295.
InParanoidiQ15427.
KOiK12831.
OMAiPVQNMMP.
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

        10         20         30         40         50
MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT
60 70 80 90 100
GQHQGYGFVE FLSEEDADYA IKIMNMIKLY GKPIRVNKAS AHNKNLDVGA
110 120 130 140 150
NIFIGNLDPE IDEKLLYDTF SAFGVILQTP KIMRDPDTGN SKGYAFINFA
160 170 180 190 200
SFDASDAAIE AMNGQYLCNR PITVSYAFKK DSKGERHGSA AERLLAAQNP
210 220 230 240 250
LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP GSFPPPVPPP
260 270 280 290 300
GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG
310 320 330 340 350
MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG
360 370 380 390 400
MPPRGPPFGS PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP
410 420
LPPPRPTPRP PVPPRGPLRG PLPQ
Length:424
Mass (Da):44,386
Last modified:November 1, 1996 - v1
Checksum:i212472A25D3FF002
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
CCDSiCCDS72900.1.
PIRiA54964.
RefSeqiNP_005841.1. NM_005850.4.
XP_005277388.1. XM_005277331.2.
UniGeneiHs.516160.

Genome annotation databases

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

Polymorphism databases

DMDMi2500587.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
CCDSiCCDS72900.1.
PIRiA54964.
RefSeqiNP_005841.1. NM_005850.4.
XP_005277388.1. XM_005277331.2.
UniGeneiHs.516160.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X5TNMR-A102-184[»]
1X5UNMR-A5-96[»]
ProteinModelPortaliQ15427.
SMRiQ15427. Positions 5-199.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115554. 103 interactions.
IntActiQ15427. 37 interactions.
MINTiMINT-1032702.
STRINGi9606.ENSP00000271628.

PTM databases

PhosphoSiteiQ15427.

Polymorphism databases

DMDMi2500587.

Proteomic databases

MaxQBiQ15427.
PaxDbiQ15427.
PeptideAtlasiQ15427.
PRIDEiQ15427.

Protocols and materials databases

DNASUi10262.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi10262.
GeneCardsiGC01M149895.
HGNCiHGNC:10771. SF3B4.
HPAiHPA028578.
MIMi154400. phenotype.
605593. gene.
neXtProtiNX_Q15427.
Orphaneti245. Nager syndrome.
PharmGKBiPA35689.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0724.
GeneTreeiENSGT00760000119302.
HOGENOMiHOG000200535.
HOVERGENiHBG002295.
InParanoidiQ15427.
KOiK12831.
OMAiPVQNMMP.
PhylomeDBiQ15427.
TreeFamiTF300890.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ15427.
GeneWikiiSF3B4.
GenomeRNAii10262.
NextBioi38880.
PROiQ15427.
SOURCEiSearch...

Gene expression databases

BgeeiQ15427.
CleanExiHS_SF3B4.
ExpressionAtlasiQ15427. baseline and differential.
GenevestigatoriQ15427.

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]
ProtoNetiSearch...

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], CLEAVAGE OF INITIATOR METHIONINE [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], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  15. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [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: March 4, 2015
This is version 159 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.