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Q15393

- SF3B3_HUMAN

UniProt

Q15393 - SF3B3_HUMAN

Protein

Splicing factor 3B subunit 3

Gene

SF3B3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 140 (01 Oct 2014)
      Sequence version 4 (17 Oct 2006)
      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. 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. nucleic acid binding Source: InterPro

    GO - Biological processi

    1. gene expression Source: Reactome
    2. mRNA processing Source: ProtInc
    3. mRNA splicing, via spliceosome Source: UniProtKB
    4. protein complex assembly Source: ProtInc
    5. RNA splicing Source: Reactome
    6. RNA splicing, via transesterification reactions Source: UniProtKB

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    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 3
    Alternative name(s):
    Pre-mRNA-splicing factor SF3b 130 kDa subunit
    Short name:
    SF3b130
    STAF130
    Spliceosome-associated protein 130
    Short name:
    SAP 130
    Gene namesi
    Name:SF3B3
    Synonyms:KIAA0017, SAP130
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 16

    Organism-specific databases

    HGNCiHGNC:10770. SF3B3.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. catalytic step 2 spliceosome Source: UniProtKB
    2. nucleoplasm Source: Reactome
    3. small nuclear ribonucleoprotein complex Source: ProtInc
    4. spliceosomal complex Source: ProtInc
    5. U12-type spliceosomal complex Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35688.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12171217Splicing factor 3B subunit 3PRO_0000218639Add
    BLAST

    Proteomic databases

    MaxQBiQ15393.
    PaxDbiQ15393.
    PeptideAtlasiQ15393.
    PRIDEiQ15393.

    PTM databases

    PhosphoSiteiQ15393.

    Expressioni

    Gene expression databases

    ArrayExpressiQ15393.
    BgeeiQ15393.
    CleanExiHS_SAP130.
    HS_SF3B3.
    GenevestigatoriQ15393.

    Organism-specific databases

    HPAiHPA042986.

    Interactioni

    Subunit structurei

    Identified in the spliceosome C complex. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. 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). Interaction between SF3B3 and SF3B1 is tighter than the interaction between SF3B3 and SF3B2. Associates with the STAGA transcription coactivator-HAT complex. Interacts with SUPT3H.6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    NUDCD3Q8IVD92EBI-346977,EBI-744342

    Protein-protein interaction databases

    BioGridi117016. 128 interactions.
    DIPiDIP-28152N.
    IntActiQ15393. 51 interactions.
    MINTiMINT-1402891.
    STRINGi9606.ENSP00000305790.

    Structurei

    3D structure databases

    ProteinModelPortaliQ15393.
    SMRiQ15393. Positions 438-769, 881-1211.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RSE1 family.Curated

    Phylogenomic databases

    eggNOGiNOG247734.
    HOGENOMiHOG000216677.
    HOVERGENiHBG093942.
    InParanoidiQ15393.
    KOiK12830.
    OMAiHPKGIRH.
    OrthoDBiEOG7N8ZTN.
    PhylomeDBiQ15393.
    TreeFamiTF105685.

    Family and domain databases

    InterProiIPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PfamiPF03178. CPSF_A. 1 hit.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 3 hits.

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q15393-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MFLYNLTLQR ATGISFAIHG NFSGTKQQEI VVSRGKILEL LRPDPNTGKV     50
    HTLLTVEVFG VIRSLMAFRL TGGTKDYIVV GSDSGRIVIL EYQPSKNMFE 100
    KIHQETFGKS GCRRIVPGQF LAVDPKGRAV MISAIEKQKL VYILNRDAAA 150
    RLTISSPLEA HKANTLVYHV VGVDVGFENP MFACLEMDYE EADNDPTGEA 200
    AANTQQTLTF YELDLGLNHV VRKYSEPLEE HGNFLITVPG GSDGPSGVLI 250
    CSENYITYKN FGDQPDIRCP IPRRRNDLDD PERGMIFVCS ATHKTKSMFF 300
    FLAQTEQGDI FKITLETDED MVTEIRLKYF DTVPVAAAMC VLKTGFLFVA 350
    SEFGNHYLYQ IAHLGDDDEE PEFSSAMPLE EGDTFFFQPR PLKNLVLVDE 400
    LDSLSPILFC QIADLANEDT PQLYVACGRG PRSSLRVLRH GLEVSEMAVS 450
    ELPGNPNAVW TVRRHIEDEF DAYIIVSFVN ATLVLSIGET VEEVTDSGFL 500
    GTTPTLSCSL LGDDALVQVY PDGIRHIRAD KRVNEWKTPG KKTIVKCAVN 550
    QRQVVIALTG GELVYFEMDP SGQLNEYTER KEMSADVVCM SLANVPPGEQ 600
    RSRFLAVGLV DNTVRIISLD PSDCLQPLSM QALPAQPESL CIVEMGGTEK 650
    QDELGERGSI GFLYLNIGLQ NGVLLRTVLD PVTGDLSDTR TRYLGSRPVK 700
    LFRVRMQGQE AVLAMSSRSW LSYSYQSRFH LTPLSYETLE FASGFASEQC 750
    PEGIVAISTN TLRILALEKL GAVFNQVAFP LQYTPRKFVI HPESNNLIII 800
    ETDHNAYTEA TKAQRKQQMA EEMVEAAGED ERELAAEMAA AFLNENLPES 850
    IFGAPKAGNG QWASVIRVMN PIQGNTLDLV QLEQNEAAFS VAVCRFSNTG 900
    EDWYVLVGVA KDLILNPRSV AGGFVYTYKL VNNGEKLEFL HKTPVEEVPA 950
    AIAPFQGRVL IGVGKLLRVY DLGKKKLLRK CENKHIANYI SGIQTIGHRV 1000
    IVSDVQESFI WVRYKRNENQ LIIFADDTYP RWVTTASLLD YDTVAGADKF 1050
    GNICVVRLPP NTNDEVDEDP TGNKALWDRG LLNGASQKAE VIMNYHVGET 1100
    VLSLQKTTLI PGGSESLVYT TLSGGIGILV PFTSHEDHDF FQHVEMHLRS 1150
    EHPPLCGRDH LSFRSYYFPV KNVIDGDLCE QFNSMEPNKQ KNVSEELDRT 1200
    PPEVSKKLED IRTRYAF 1217
    Length:1,217
    Mass (Da):135,577
    Last modified:October 17, 2006 - v4
    Checksum:i35CACAF5ACC32512
    GO
    Isoform 2 (identifier: Q15393-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         250-275: ICSENYITYKNFGDQPDIRCPIPRRR → NLSPPFPKAIPALICLDSPVYFCTHP
         276-1217: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:275
    Mass (Da):30,210
    Checksum:iD46811A34E142E7D
    GO
    Isoform 3 (identifier: Q15393-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-818: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:399
    Mass (Da):44,606
    Checksum:iE8F6C071997055A0
    GO

    Sequence cautioni

    The sequence BAA02805.1 differs from that shown. Reason: Erroneous initiation.
    The sequence BAA32662.2 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti193 – 1931D → G in CAB56791. (PubMed:10490618)Curated
    Sequence conflicti301 – 3011F → S in AAH68974. (PubMed:15489334)Curated
    Sequence conflicti302 – 3021L → W in CAB56791. (PubMed:10490618)Curated
    Sequence conflicti899 – 8991T → I in AAH00463. (PubMed:15489334)Curated
    Sequence conflicti899 – 8991T → I in AAH03146. (PubMed:15489334)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti908 – 9081G → R.
    Corresponds to variant rs11551673 [ dbSNP | Ensembl ].
    VAR_053647

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 818818Missing in isoform 3. 1 PublicationVSP_022977Add
    BLAST
    Alternative sequencei250 – 27526ICSEN…IPRRR → NLSPPFPKAIPALICLDSPV YFCTHP in isoform 2. 1 PublicationVSP_022978Add
    BLAST
    Alternative sequencei276 – 1217942Missing in isoform 2. 1 PublicationVSP_022979Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ001443 mRNA. Translation: CAB56791.1.
    D87686 mRNA. Translation: BAA32662.2. Different initiation.
    D13642 mRNA. Translation: BAA02805.1. Different initiation.
    BC000463 mRNA. Translation: AAH00463.1.
    BC003146 mRNA. Translation: AAH03146.1.
    BC009780 mRNA. Translation: AAH09780.1.
    BC068974 mRNA. Translation: AAH68974.1.
    AL110251 mRNA. Translation: CAB53699.1.
    CCDSiCCDS10894.1. [Q15393-1]
    PIRiT14779.
    RefSeqiNP_036558.3. NM_012426.4. [Q15393-1]
    UniGeneiHs.514435.

    Genome annotation databases

    EnsembliENST00000302516; ENSP00000305790; ENSG00000189091. [Q15393-1]
    GeneIDi23450.
    KEGGihsa:23450.
    UCSCiuc002ezf.3. human. [Q15393-1]

    Polymorphism databases

    DMDMi116242787.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ001443 mRNA. Translation: CAB56791.1 .
    D87686 mRNA. Translation: BAA32662.2 . Different initiation.
    D13642 mRNA. Translation: BAA02805.1 . Different initiation.
    BC000463 mRNA. Translation: AAH00463.1 .
    BC003146 mRNA. Translation: AAH03146.1 .
    BC009780 mRNA. Translation: AAH09780.1 .
    BC068974 mRNA. Translation: AAH68974.1 .
    AL110251 mRNA. Translation: CAB53699.1 .
    CCDSi CCDS10894.1. [Q15393-1 ]
    PIRi T14779.
    RefSeqi NP_036558.3. NM_012426.4. [Q15393-1 ]
    UniGenei Hs.514435.

    3D structure databases

    ProteinModelPortali Q15393.
    SMRi Q15393. Positions 438-769, 881-1211.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 117016. 128 interactions.
    DIPi DIP-28152N.
    IntActi Q15393. 51 interactions.
    MINTi MINT-1402891.
    STRINGi 9606.ENSP00000305790.

    Chemistry

    BindingDBi Q15393.
    ChEMBLi CHEMBL1250378.

    PTM databases

    PhosphoSitei Q15393.

    Polymorphism databases

    DMDMi 116242787.

    Proteomic databases

    MaxQBi Q15393.
    PaxDbi Q15393.
    PeptideAtlasi Q15393.
    PRIDEi Q15393.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000302516 ; ENSP00000305790 ; ENSG00000189091 . [Q15393-1 ]
    GeneIDi 23450.
    KEGGi hsa:23450.
    UCSCi uc002ezf.3. human. [Q15393-1 ]

    Organism-specific databases

    CTDi 23450.
    GeneCardsi GC16P070557.
    HGNCi HGNC:10770. SF3B3.
    HPAi HPA042986.
    MIMi 605592. gene.
    neXtProti NX_Q15393.
    PharmGKBi PA35688.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG247734.
    HOGENOMi HOG000216677.
    HOVERGENi HBG093942.
    InParanoidi Q15393.
    KOi K12830.
    OMAi HPKGIRH.
    OrthoDBi EOG7N8ZTN.
    PhylomeDBi Q15393.
    TreeFami TF105685.

    Enzyme and pathway databases

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

    Miscellaneous databases

    GeneWikii SF3B3.
    GenomeRNAii 23450.
    NextBioi 45731.
    PROi Q15393.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q15393.
    Bgeei Q15393.
    CleanExi HS_SAP130.
    HS_SF3B3.
    Genevestigatori Q15393.

    Family and domain databases

    InterProi IPR004871. Cleavage/polyA-sp_fac_asu_C.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    Pfami PF03178. CPSF_A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 3 hits.
    ProtoNeti Search...

    Publicationsi

    1. "Characterization of a protein complex containing spliceosomal proteins saps 49,130,145 and 155."
      Das B.K., Xia L., Palandjian L., Gozani O., Chyung Y., Reed R.
      Mol. Cell. Biol. 19:6796-6802(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1."
      Nomura N., Miyajima N., Sazuka T., Tanaka A., Kawarabayasi Y., Sato S., Nagase T., Seki N., Ishikawa K., Tabata S.
      DNA Res. 1:27-35(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Bone marrow.
    3. Nomura N.
      Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION.
    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] (ISOFORMS 1; 2 AND 3).
      Tissue: Lung, Skeletal muscle and Skin.
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1003-1217 (ISOFORM 1).
      Tissue: Testis.
    6. "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo."
      Martinez E., Palhan V.B., Tjernberg A., Lymar E.S., Gamper A.M., Kundu T.K., Chait B.T., Roeder R.G.
      Mol. Cell. Biol. 21:6782-6795(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, INTERACTION WITH SUPT3H, INTERACTION WITH THE STAGA COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
    7. "The TFIID components human TAFII140 and Drosophila BIP2 (TAFII155) are novel metazoan homologues of yeast TAFII47 containing a histone fold and a PHD finger."
      Gangloff Y.G., Pointud J.-C., Thuault S., Carre L., Romier C., Muratoglu S., Brand M., Tora L., Couderc J.-L., Davidson I.
      Mol. Cell. Biol. 21:5109-5121(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TAF3.
    8. "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.
    9. "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
      Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
      RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
    10. "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.
    11. "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.
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSF3B3_HUMAN
    AccessioniPrimary (citable) accession number: Q15393
    Secondary accession number(s): Q6NTI8
    , Q96GC0, Q9BPY2, Q9UFX7, Q9UJ29
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: October 17, 2006
    Last modified: October 1, 2014
    This is version 140 of the entry and version 4 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

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 16
      Human chromosome 16: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3