Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q96DI7

- SNR40_HUMAN

UniProt

Q96DI7 - SNR40_HUMAN

Protein

U5 small nuclear ribonucleoprotein 40 kDa protein

Gene

SNRNP40

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 128 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.1 Publication

    GO - Molecular functioni

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

    GO - Biological processi

    1. gene expression Source: Reactome
    2. mRNA splicing, via spliceosome Source: UniProtKB
    3. RNA processing Source: ProtInc
    4. RNA splicing Source: Reactome
    5. 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.
    SignaLinkiQ96DI7.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U5 small nuclear ribonucleoprotein 40 kDa protein
    Short name:
    U5 snRNP 40 kDa protein
    Short name:
    U5-40K
    Alternative name(s):
    38 kDa-splicing factor
    Prp8-binding protein
    Short name:
    hPRP8BP
    U5 snRNP-specific 40 kDa protein
    WD repeat-containing protein 57
    Gene namesi
    Name:SNRNP40
    Synonyms:PRP8BP, SFP38, WDR57
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:30857. SNRNP40.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. catalytic step 2 spliceosome Source: UniProtKB
    2. cytoplasm Source: HPA
    3. nucleoplasm Source: Reactome
    4. nucleus Source: HPA
    5. small nucleolar ribonucleoprotein complex Source: UniProtKB
    6. U5 snRNP Source: ProtInc

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA164726132.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 357357U5 small nuclear ribonucleoprotein 40 kDa proteinPRO_0000051417Add
    BLAST

    Proteomic databases

    MaxQBiQ96DI7.
    PaxDbiQ96DI7.
    PeptideAtlasiQ96DI7.
    PRIDEiQ96DI7.

    PTM databases

    PhosphoSiteiQ96DI7.

    Expressioni

    Gene expression databases

    ArrayExpressiQ96DI7.
    BgeeiQ96DI7.
    CleanExiHS_SNRNP40.
    GenevestigatoriQ96DI7.

    Organism-specific databases

    HPAiHPA026527.
    HPA027345.

    Interactioni

    Subunit structurei

    Identified in the spliceosome C complex. Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PRPF8Q6P2Q93EBI-538492,EBI-538479

    Protein-protein interaction databases

    BioGridi114805. 39 interactions.
    IntActiQ96DI7. 21 interactions.
    MINTiMINT-1410013.
    STRINGi9606.ENSP00000263694.

    Structurei

    3D structure databases

    ProteinModelPortaliQ96DI7.
    SMRiQ96DI7. Positions 9-349.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati64 – 10340WD 1Add
    BLAST
    Repeati107 – 14640WD 2Add
    BLAST
    Repeati149 – 18941WD 3Add
    BLAST
    Repeati191 – 23040WD 4Add
    BLAST
    Repeati233 – 27240WD 5Add
    BLAST
    Repeati283 – 32240WD 6Add
    BLAST
    Repeati325 – 35733WD 7Add
    BLAST

    Sequence similaritiesi

    Contains 7 WD repeats.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, WD repeat

    Phylogenomic databases

    eggNOGiCOG2319.
    HOGENOMiHOG000091644.
    HOVERGENiHBG105197.
    InParanoidiQ96DI7.
    KOiK12857.
    OrthoDBiEOG7992QT.
    PhylomeDBiQ96DI7.
    TreeFamiTF300039.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR020472. G-protein_beta_WD-40_rep.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR019775. WD40_repeat_CS.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PfamiPF00400. WD40. 7 hits.
    [Graphical view]
    PRINTSiPR00320. GPROTEINBRPT.
    SMARTiSM00320. WD40. 7 hits.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 1 hit.
    PROSITEiPS00678. WD_REPEATS_1. 5 hits.
    PS50082. WD_REPEATS_2. 7 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q96DI7-1) [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

    MIEQQKRKGP ELPLVPVKRQ RHELLLGAGS GPGAGQQQAT PGALLQAGPP    50
    RCSSLQAPIM LLSGHEGEVY CCKFHPNGST LASAGFDRLI LLWNVYGDCD 100
    NYATLKGHSG AVMELHYNTD GSMLFSASTD KTVAVWDSET GERVKRLKGH 150
    TSFVNSCYPA RRGPQLVCTG SDDGTVKLWD IRKKAAIQTF QNTYQVLAVT 200
    FNDTSDQIIS GGIDNDIKVW DLRQNKLTYT MRGHADSVTG LSLSSEGSYL 250
    LSNAMDNTVR VWDVRPFAPK ERCVKIFQGN VHNFEKNLLR CSWSPDGSKI 300
    AAGSADRFVY VWDTTSRRIL YKLPGHAGSI NEVAFHPDEP IIISASSDKR 350
    LYMGEIQ 357
    Length:357
    Mass (Da):39,311
    Last modified:December 1, 2001 - v1
    Checksum:iDE8CADEB098E560C
    GO
    Isoform 2 (identifier: Q96DI7-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         343-357: ISASSDKRLYMGEIQ → ETGFHRIGQG...ESKSNAPFSS

    Note: No experimental confirmation available.

    Show »
    Length:409
    Mass (Da):44,516
    Checksum:i06BC77CD284995FF
    GO

    Sequence cautioni

    The sequence AAC64084.1 differs from that shown. Reason: Frameshift at position 319. An insertion/deletion of a short nucleotide stretch in its cDNA resulting in a frameshift.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti3 – 31E → D in AAC69625. (PubMed:9774689)Curated
    Sequence conflicti162 – 1632RG → KS in AAC69625. (PubMed:9774689)Curated
    Sequence conflicti187 – 1871I → V in AAC64084. (PubMed:9731529)Curated
    Sequence conflicti343 – 3431I → L(PubMed:9731529)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei343 – 35715ISASS…MGEIQ → ETGFHRIGQGGHELLTSSNP PASASQSAGITGVSHCAQLQ TVFMWVSMSVSPLLISGESK SNAPFSS in isoform 2. 1 PublicationVSP_056395Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF090988 mRNA. Translation: AAC69625.1.
    AK298823 mRNA. Translation: BAG60953.1.
    AL451070, AC114495 Genomic DNA. Translation: CAH71848.1.
    BC001494 mRNA. Translation: AAH01494.1.
    AF083383 mRNA. Translation: AAC64084.1. Sequence problems.
    CCDSiCCDS340.1.
    RefSeqiNP_004805.2. NM_004814.2.
    UniGeneiHs.33962.

    Genome annotation databases

    EnsembliENST00000263694; ENSP00000263694; ENSG00000060688.
    ENST00000446633; ENSP00000406841; ENSG00000060688.
    GeneIDi9410.
    KEGGihsa:9410.
    UCSCiuc001bso.3. human.

    Polymorphism databases

    DMDMi67462075.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF090988 mRNA. Translation: AAC69625.1 .
    AK298823 mRNA. Translation: BAG60953.1 .
    AL451070 , AC114495 Genomic DNA. Translation: CAH71848.1 .
    BC001494 mRNA. Translation: AAH01494.1 .
    AF083383 mRNA. Translation: AAC64084.1 . Sequence problems.
    CCDSi CCDS340.1.
    RefSeqi NP_004805.2. NM_004814.2.
    UniGenei Hs.33962.

    3D structure databases

    ProteinModelPortali Q96DI7.
    SMRi Q96DI7. Positions 9-349.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114805. 39 interactions.
    IntActi Q96DI7. 21 interactions.
    MINTi MINT-1410013.
    STRINGi 9606.ENSP00000263694.

    PTM databases

    PhosphoSitei Q96DI7.

    Polymorphism databases

    DMDMi 67462075.

    Proteomic databases

    MaxQBi Q96DI7.
    PaxDbi Q96DI7.
    PeptideAtlasi Q96DI7.
    PRIDEi Q96DI7.

    Protocols and materials databases

    DNASUi 9410.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000263694 ; ENSP00000263694 ; ENSG00000060688 .
    ENST00000446633 ; ENSP00000406841 ; ENSG00000060688 .
    GeneIDi 9410.
    KEGGi hsa:9410.
    UCSCi uc001bso.3. human.

    Organism-specific databases

    CTDi 9410.
    GeneCardsi GC01M031732.
    HGNCi HGNC:30857. SNRNP40.
    HPAi HPA026527.
    HPA027345.
    MIMi 607797. gene.
    neXtProti NX_Q96DI7.
    PharmGKBi PA164726132.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2319.
    HOGENOMi HOG000091644.
    HOVERGENi HBG105197.
    InParanoidi Q96DI7.
    KOi K12857.
    OrthoDBi EOG7992QT.
    PhylomeDBi Q96DI7.
    TreeFami TF300039.

    Enzyme and pathway databases

    Reactomei REACT_1753. mRNA Splicing - Minor Pathway.
    REACT_467. mRNA Splicing - Major Pathway.
    SignaLinki Q96DI7.

    Miscellaneous databases

    ChiTaRSi SNRNP40. human.
    GeneWikii WDR57.
    GenomeRNAii 9410.
    NextBioi 35252.
    PROi Q96DI7.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q96DI7.
    Bgeei Q96DI7.
    CleanExi HS_SNRNP40.
    Genevestigatori Q96DI7.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR020472. G-protein_beta_WD-40_rep.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR019775. WD40_repeat_CS.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    Pfami PF00400. WD40. 7 hits.
    [Graphical view ]
    PRINTSi PR00320. GPROTEINBRPT.
    SMARTi SM00320. WD40. 7 hits.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 1 hit.
    PROSITEi PS00678. WD_REPEATS_1. 5 hits.
    PS50082. WD_REPEATS_2. 7 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein."
      Achsel T., Ahrens K., Brahms H., Teigelkamp S., Luehrmann R.
      Mol. Cell. Biol. 18:6756-6766(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, IDENTIFICATION IN U5 SNRP COMPLEX, INTERACTION WITH PRPF8.
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    3. "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].
    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] (ISOFORM 1).
      Tissue: Placenta.
    5. "Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex."
      Neubauer G., King A., Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A.I., Mann M.
      Nat. Genet. 20:46-50(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-357 (ISOFORM 1), IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, IDENTIFICATION IN SPLICEOSOMAL COMPLEX.
    6. "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 SPLICEOSOME C COMPLEX.
    7. "The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
      Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
      RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSNR40_HUMAN
    AccessioniPrimary (citable) accession number: Q96DI7
    Secondary accession number(s): B4DQJ1, O75938, O95320
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 128 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

    Complete proteome, 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3