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Protein

U6 snRNA-associated Sm-like protein LSm2

Gene

LSM2

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

Functioni

Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB
  2. Ral GTPase binding Source: UniProtKB
  3. U6 snRNA binding Source: UniProtKB

GO - Biological processi

  1. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
  2. gene expression Source: Reactome
  3. mRNA splicing, via spliceosome Source: UniProtKB
  4. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
  5. RNA splicing Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_20518. mRNA decay by 5' to 3' exoribonuclease.
REACT_467. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm2
Alternative name(s):
Protein G7b
Small nuclear ribonuclear protein D homolog
snRNP core Sm-like protein Sm-x5
Gene namesi
Name:LSM2
Synonyms:C6orf28, G7B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 6, UP000005640: Unplaced

Organism-specific databases

HGNCiHGNC:13940. LSM2.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. catalytic step 2 spliceosome Source: UniProtKB
  2. cytosol Source: Reactome
  3. nucleoplasm Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA25929.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9595U6 snRNA-associated Sm-like protein LSm2PRO_0000125556Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei79 – 791Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9Y333.
PaxDbiQ9Y333.
PeptideAtlasiQ9Y333.
PRIDEiQ9Y333.

PTM databases

PhosphoSiteiQ9Y333.

Expressioni

Gene expression databases

BgeeiQ9Y333.
CleanExiHS_LSM2.
GenevestigatoriQ9Y333.

Organism-specific databases

HPAiHPA052805.
HPA066718.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. LSm subunits form a heteromer with a doughnut shape.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1O151163EBI-347416,EBI-347619
LSM3P6231011EBI-347416,EBI-348239
LSM7Q9UK455EBI-347416,EBI-348372
LSM8O957776EBI-347416,EBI-347779
SNRPD2P623163EBI-347416,EBI-297993
ZNF408Q9H9D44EBI-347416,EBI-347633

Protein-protein interaction databases

BioGridi121778. 53 interactions.
DIPiDIP-31139N.
IntActiQ9Y333. 26 interactions.
MINTiMINT-1032572.
STRINGi9606.ENSP00000364813.

Structurei

3D structure databases

ProteinModelPortaliQ9Y333.
SMRiQ9Y333. Positions 1-89.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000016597.
HOGENOMiHOG000166937.
HOVERGENiHBG000486.
InParanoidiQ9Y333.
KOiK12621.
OMAiDCTLLQD.
OrthoDBiEOG7DNNXM.
PhylomeDBiQ9Y333.
TreeFamiTF314960.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERiPTHR13829. PTHR13829. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9Y333-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFYSFFKSL VGKDVVVELK NDLSICGTLH SVDQYLNIKL TDISVTDPEK
60 70 80 90
YPHMLSVKNC FIRGSVVRYV QLPADEVDTQ LLQDAARKEA LQQKQ
Length:95
Mass (Da):10,835
Last modified:November 1, 1999 - v1
Checksum:i623591A09A6ABACE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF182288 mRNA. Translation: AAD56226.1.
AJ245416 mRNA. Translation: CAB52190.1.
AF196468 mRNA. Translation: AAG33023.1.
AF134726 Genomic DNA. Translation: AAD21818.1.
BA000025 Genomic DNA. Translation: BAB63302.1.
AF136977 mRNA. Translation: AAG49438.1.
CR542146 mRNA. Translation: CAG46943.1.
CR542157 mRNA. Translation: CAG46954.1.
AL929592 Genomic DNA. Translation: CAI18462.1.
CR759915 Genomic DNA. Translation: CAQ07255.1.
CR759787 Genomic DNA. Translation: CAQ10128.1.
CR925765 Genomic DNA. Translation: CAQ10626.1.
CH471081 Genomic DNA. Translation: EAX03525.1.
BC009192 mRNA. Translation: AAH09192.1.
CCDSiCCDS4722.1.
RefSeqiNP_067000.1. NM_021177.4.
UniGeneiHs.103106.

Genome annotation databases

EnsembliENST00000375661; ENSP00000364813; ENSG00000204392.
ENST00000383391; ENSP00000372883; ENSG00000172850.
ENST00000424975; ENSP00000403345; ENSG00000231502.
ENST00000432122; ENSP00000414006; ENSG00000224979.
ENST00000434125; ENSP00000406280; ENSG00000225998.
ENST00000455705; ENSP00000414634; ENSG00000236826.
GeneIDi57819.
KEGGihsa:57819.
UCSCiuc003nxg.3. human.

Polymorphism databases

DMDMi10720079.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF182288 mRNA. Translation: AAD56226.1.
AJ245416 mRNA. Translation: CAB52190.1.
AF196468 mRNA. Translation: AAG33023.1.
AF134726 Genomic DNA. Translation: AAD21818.1.
BA000025 Genomic DNA. Translation: BAB63302.1.
AF136977 mRNA. Translation: AAG49438.1.
CR542146 mRNA. Translation: CAG46943.1.
CR542157 mRNA. Translation: CAG46954.1.
AL929592 Genomic DNA. Translation: CAI18462.1.
CR759915 Genomic DNA. Translation: CAQ07255.1.
CR759787 Genomic DNA. Translation: CAQ10128.1.
CR925765 Genomic DNA. Translation: CAQ10626.1.
CH471081 Genomic DNA. Translation: EAX03525.1.
BC009192 mRNA. Translation: AAH09192.1.
CCDSiCCDS4722.1.
RefSeqiNP_067000.1. NM_021177.4.
UniGeneiHs.103106.

3D structure databases

ProteinModelPortaliQ9Y333.
SMRiQ9Y333. Positions 1-89.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121778. 53 interactions.
DIPiDIP-31139N.
IntActiQ9Y333. 26 interactions.
MINTiMINT-1032572.
STRINGi9606.ENSP00000364813.

PTM databases

PhosphoSiteiQ9Y333.

Polymorphism databases

DMDMi10720079.

Proteomic databases

MaxQBiQ9Y333.
PaxDbiQ9Y333.
PeptideAtlasiQ9Y333.
PRIDEiQ9Y333.

Protocols and materials databases

DNASUi57819.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000375661; ENSP00000364813; ENSG00000204392.
ENST00000383391; ENSP00000372883; ENSG00000172850.
ENST00000424975; ENSP00000403345; ENSG00000231502.
ENST00000432122; ENSP00000414006; ENSG00000224979.
ENST00000434125; ENSP00000406280; ENSG00000225998.
ENST00000455705; ENSP00000414634; ENSG00000236826.
GeneIDi57819.
KEGGihsa:57819.
UCSCiuc003nxg.3. human.

Organism-specific databases

CTDi57819.
GeneCardsiGC06M031765.
GC06Mi31776.
GC06Mj31752.
GC06Mk31747.
GC06Mm31841.
GC06Mn31755.
HGNCiHGNC:13940. LSM2.
HPAiHPA052805.
HPA066718.
MIMi607282. gene.
neXtProtiNX_Q9Y333.
PharmGKBiPA25929.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000016597.
HOGENOMiHOG000166937.
HOVERGENiHBG000486.
InParanoidiQ9Y333.
KOiK12621.
OMAiDCTLLQD.
OrthoDBiEOG7DNNXM.
PhylomeDBiQ9Y333.
TreeFamiTF314960.

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_20518. mRNA decay by 5' to 3' exoribonuclease.
REACT_467. mRNA Splicing - Major Pathway.

Miscellaneous databases

GeneWikiiLSM2.
GenomeRNAii57819.
NextBioi64772.
PROiQ9Y333.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y333.
CleanExiHS_LSM2.
GenevestigatoriQ9Y333.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERiPTHR13829. PTHR13829. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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], PARTIAL PROTEIN SEQUENCE.
  2. "Characterisation of the novel gene G7b located in the class III region of the human major histocompatibility complex."
    Olavesen M.G., Campbell R.D.
    Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "Human SMX5 homolog."
    Schmarda A., Fresser F., Paulmichl M.
    Submitted (OCT-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse."
    Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., Hood L.
    Genome Res. 13:2621-2636(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region."
    Shiina S., Tamiya G., Oka A., Inoko H.
    Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Hypothalamus.
  7. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  8. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  9. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  10. "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: Placenta.
  11. "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.
  12. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-79, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic kidney.
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiLSM2_HUMAN
AccessioniPrimary (citable) accession number: Q9Y333
Secondary accession number(s): Q6FGG1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1999
Last modified: March 4, 2015
This is version 146 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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.