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Protein

U6 snRNA-associated Sm-like protein LSm5

Gene

LSM5

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

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

  • RNA binding Source: ProtInc

GO - Biological processi

Complete GO annotation...

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 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:17162. LSM5.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • nucleus Source: ProtInc
  • spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134881171.

Polymorphism and mutation databases

BioMutaiLSM5.
DMDMi10720081.

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

BgeeiQ9Y4Y9.
CleanExiHS_LSM5.
ExpressionAtlasiQ9Y4Y9. baseline and differential.
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
LSM6P623127EBI-373007,EBI-373310
LSM7Q9UK4510EBI-373007,EBI-348372
SNRPFP623066EBI-373007,EBI-356900

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.
GeneTreeiENSGT00390000001455.
HOVERGENiHBG107310.
InParanoidiQ9Y4Y9.
KOiK12624.
OMAiHIVMKND.
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. AlignAdd to basket

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

        10         20         30         40         50
MAANATTNPS QLLPLELVDK CIGSRIHIVM KSDKEIVGTL LGFDDFVNMV
60 70 80 90
LEDVTEFEIT PEGRRITKLD QILLNGNNIT MLVPGGEGPE V
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:
EMBLi
GenBanki
DDBJi
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]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

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

PTM databases

PhosphoSiteiQ9Y4Y9.

Polymorphism and mutation databases

BioMutaiLSM5.
DMDMi10720081.

Proteomic databases

MaxQBiQ9Y4Y9.
PaxDbiQ9Y4Y9.
PRIDEiQ9Y4Y9.

Protocols and materials databases

DNASUi23658.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi23658.
GeneCardsiGC07M032524.
HGNCiHGNC:17162. LSM5.
HPAiHPA019054.
MIMi607285. gene.
neXtProtiNX_Q9Y4Y9.
PharmGKBiPA134881171.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000001455.
HOVERGENiHBG107310.
InParanoidiQ9Y4Y9.
KOiK12624.
OMAiHIVMKND.
OrthoDBiEOG7NSB4W.
PhylomeDBiQ9Y4Y9.
TreeFamiTF313575.

Enzyme and pathway databases

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

Miscellaneous databases

GeneWikiiLSM5.
GenomeRNAii23658.
NextBioi46501.
PROiQ9Y4Y9.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y4Y9.
CleanExiHS_LSM5.
ExpressionAtlasiQ9Y4Y9. baseline and differential.
GenevestigatoriQ9Y4Y9.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [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: April 29, 2015
This is version 132 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

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.