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Q15427

- SF3B4_HUMAN

UniProt

Q15427 - SF3B4_HUMAN

Protein

Splicing factor 3B subunit 4

Gene

SF3B4

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 154 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    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

    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

    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.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.

    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

    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.
    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.
    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.
    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 .
    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

    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: October 1, 2014
    This is version 154 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