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Q9Y4Y9

- LSM5_HUMAN

UniProt

Q9Y4Y9 - LSM5_HUMAN

Protein

U6 snRNA-associated Sm-like protein LSm5

Gene

LSM5

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Plays a role in U6 snRNP assembly and function. Binds to the 3' end of U6 snRNA, thereby facilitating formation of the spliceosomal U4/U6 duplex formation in vitro.

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. RNA binding Source: ProtInc

    GO - Biological processi

    1. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
    2. gene expression Source: Reactome
    3. mRNA metabolic process Source: Reactome
    4. mRNA processing Source: ProtInc
    5. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
    6. RNA metabolic process Source: Reactome
    7. RNA splicing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Ribonucleoprotein

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_20518. mRNA decay by 5' to 3' exoribonuclease.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm5
    Gene namesi
    Name:LSM5
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 7

    Organism-specific databases

    HGNCiHGNC:17162. LSM5.

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. cytosol Source: Reactome
    2. nucleus Source: ProtInc
    3. spliceosomal complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134881171.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed3 Publications
    Chaini2 – 9190U6 snRNA-associated Sm-like protein LSm5PRO_0000125572Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine3 Publications

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ9Y4Y9.
    PaxDbiQ9Y4Y9.
    PRIDEiQ9Y4Y9.

    PTM databases

    PhosphoSiteiQ9Y4Y9.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9Y4Y9.
    BgeeiQ9Y4Y9.
    CleanExiHS_LSM5.
    GenevestigatoriQ9Y4Y9.

    Organism-specific databases

    HPAiHPA019054.

    Interactioni

    Subunit structurei

    LSm subunits form a heteromer with a doughnut shape.By similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LSM3P623103EBI-373007,EBI-348239
    LSM6P623124EBI-373007,EBI-373310
    LSM7Q9UK455EBI-373007,EBI-348372

    Protein-protein interaction databases

    BioGridi117180. 18 interactions.
    DIPiDIP-31162N.
    IntActiQ9Y4Y9. 7 interactions.
    MINTiMINT-3086779.
    STRINGi9606.ENSP00000410758.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Y4Y9.
    SMRiQ9Y4Y9. Positions 12-86.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the snRNP Sm proteins family.Curated

    Phylogenomic databases

    eggNOGiCOG1958.
    HOVERGENiHBG107310.
    InParanoidiQ9Y4Y9.
    KOiK12624.
    OMAiCIGSKIH.
    OrthoDBiEOG7NSB4W.
    PhylomeDBiQ9Y4Y9.
    TreeFamiTF313575.

    Family and domain databases

    InterProiIPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view]
    PfamiPF01423. LSM. 1 hit.
    [Graphical view]
    SMARTiSM00651. Sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF50182. SSF50182. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

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

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9Y4Y9-1) [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

    MAANATTNPS QLLPLELVDK CIGSRIHIVM KSDKEIVGTL LGFDDFVNMV   50
    LEDVTEFEIT PEGRRITKLD QILLNGNNIT MLVPGGEGPE V 91
    Length:91
    Mass (Da):9,937
    Last modified:January 23, 2007 - v3
    Checksum:i82B5C8830E64C992
    GO
    Isoform 2 (identifier: Q9Y4Y9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-29: Missing.

    Show »
    Length:62
    Mass (Da):6,850
    Checksum:i6340D862682806E2
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 2929Missing in isoform 2. 1 PublicationVSP_040991Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ238097 mRNA. Translation: CAB45868.1.
    AF182291 mRNA. Translation: AAD56229.1.
    AC018641 Genomic DNA. No translation available.
    BC005938 mRNA. Translation: AAH05938.1.
    BF701546 mRNA. No translation available.
    CCDSiCCDS47571.1. [Q9Y4Y9-2]
    CCDS5438.1. [Q9Y4Y9-1]
    RefSeqiNP_001124182.1. NM_001130710.1. [Q9Y4Y9-2]
    NP_001132971.1. NM_001139499.1. [Q9Y4Y9-2]
    NP_036454.1. NM_012322.2. [Q9Y4Y9-1]
    UniGeneiHs.424908.

    Genome annotation databases

    EnsembliENST00000409292; ENSP00000386814; ENSG00000106355. [Q9Y4Y9-2]
    ENST00000409782; ENSP00000387109; ENSG00000106355. [Q9Y4Y9-2]
    ENST00000409909; ENSP00000386363; ENSG00000106355. [Q9Y4Y9-2]
    ENST00000409952; ENSP00000387126; ENSG00000106355. [Q9Y4Y9-2]
    ENST00000410044; ENSP00000386707; ENSG00000106355. [Q9Y4Y9-2]
    ENST00000450169; ENSP00000410758; ENSG00000106355. [Q9Y4Y9-1]
    GeneIDi23658.
    KEGGihsa:23658.
    UCSCiuc003tct.2. human. [Q9Y4Y9-1]

    Polymorphism databases

    DMDMi10720081.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ238097 mRNA. Translation: CAB45868.1 .
    AF182291 mRNA. Translation: AAD56229.1 .
    AC018641 Genomic DNA. No translation available.
    BC005938 mRNA. Translation: AAH05938.1 .
    BF701546 mRNA. No translation available.
    CCDSi CCDS47571.1. [Q9Y4Y9-2 ]
    CCDS5438.1. [Q9Y4Y9-1 ]
    RefSeqi NP_001124182.1. NM_001130710.1. [Q9Y4Y9-2 ]
    NP_001132971.1. NM_001139499.1. [Q9Y4Y9-2 ]
    NP_036454.1. NM_012322.2. [Q9Y4Y9-1 ]
    UniGenei Hs.424908.

    3D structure databases

    ProteinModelPortali Q9Y4Y9.
    SMRi Q9Y4Y9. Positions 12-86.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 117180. 18 interactions.
    DIPi DIP-31162N.
    IntActi Q9Y4Y9. 7 interactions.
    MINTi MINT-3086779.
    STRINGi 9606.ENSP00000410758.

    PTM databases

    PhosphoSitei Q9Y4Y9.

    Polymorphism databases

    DMDMi 10720081.

    Proteomic databases

    MaxQBi Q9Y4Y9.
    PaxDbi Q9Y4Y9.
    PRIDEi Q9Y4Y9.

    Protocols and materials databases

    DNASUi 23658.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000409292 ; ENSP00000386814 ; ENSG00000106355 . [Q9Y4Y9-2 ]
    ENST00000409782 ; ENSP00000387109 ; ENSG00000106355 . [Q9Y4Y9-2 ]
    ENST00000409909 ; ENSP00000386363 ; ENSG00000106355 . [Q9Y4Y9-2 ]
    ENST00000409952 ; ENSP00000387126 ; ENSG00000106355 . [Q9Y4Y9-2 ]
    ENST00000410044 ; ENSP00000386707 ; ENSG00000106355 . [Q9Y4Y9-2 ]
    ENST00000450169 ; ENSP00000410758 ; ENSG00000106355 . [Q9Y4Y9-1 ]
    GeneIDi 23658.
    KEGGi hsa:23658.
    UCSCi uc003tct.2. human. [Q9Y4Y9-1 ]

    Organism-specific databases

    CTDi 23658.
    GeneCardsi GC07M032524.
    HGNCi HGNC:17162. LSM5.
    HPAi HPA019054.
    MIMi 607285. gene.
    neXtProti NX_Q9Y4Y9.
    PharmGKBi PA134881171.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1958.
    HOVERGENi HBG107310.
    InParanoidi Q9Y4Y9.
    KOi K12624.
    OMAi CIGSKIH.
    OrthoDBi EOG7NSB4W.
    PhylomeDBi Q9Y4Y9.
    TreeFami TF313575.

    Enzyme and pathway databases

    Reactomei REACT_20518. mRNA decay by 5' to 3' exoribonuclease.

    Miscellaneous databases

    GeneWikii LSM5.
    GenomeRNAii 23658.
    NextBioi 46501.
    PROi Q9Y4Y9.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Y4Y9.
    Bgeei Q9Y4Y9.
    CleanExi HS_LSM5.
    Genevestigatori Q9Y4Y9.

    Family and domain databases

    InterProi IPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view ]
    Pfami PF01423. LSM. 1 hit.
    [Graphical view ]
    SMARTi SM00651. Sm. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50182. SSF50182. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
      Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
      EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Placenta.
    2. "A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro."
      Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., Luehrmann R.
      EMBO J. 18:5789-5802(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PARTIAL PROTEIN SEQUENCE.
    3. "The DNA sequence of human chromosome 7."
      Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
      , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
      Nature 424:157-164(2003) [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] (ISOFORMS 1 AND 2).
      Tissue: Bone marrow and Brain.
    5. "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].
    6. "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].
    7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiLSM5_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y4Y9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 128 of the entry and version 3 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, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 7
      Human chromosome 7: 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