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Protein

U6 snRNA-associated Sm-like protein LSm1

Gene

LSM1

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

Functioni

Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.1 Publication

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB
  2. RNA cap binding Source: GO_Central

GO - Biological processi

  1. deadenylation-dependent decapping of nuclear-transcribed mRNA Source: GO_Central
  2. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
  3. gene expression Source: Reactome
  4. histone mRNA catabolic process Source: UniProtKB
  5. mRNA metabolic process Source: Reactome
  6. mRNA processing Source: ProtInc
  7. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
  8. RNA metabolic process Source: Reactome
  9. RNA splicing Source: ProtInc
  10. RNA splicing, via transesterification reactions Source: UniProtKB
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 LSm1
Alternative name(s):
Cancer-associated Sm-like
Small nuclear ribonuclear CaSm
Gene namesi
Name:LSM1
Synonyms:CASM
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 8

Organism-specific databases

HGNCiHGNC:20472. LSM1.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. cytoplasm Source: MGI
  2. cytoplasmic mRNA processing body Source: GO_Central
  3. cytosol Source: Reactome
  4. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134864226.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 133133U6 snRNA-associated Sm-like protein LSm1PRO_0000125554Add
BLAST

Proteomic databases

MaxQBiO15116.
PaxDbiO15116.
PeptideAtlasiO15116.
PRIDEiO15116.

PTM databases

PhosphoSiteiO15116.

Expressioni

Tissue specificityi

Has elevated expression in pancreatic cancer and in several cancer-derived cell lines.

Gene expression databases

BgeeiO15116.
CleanExiHS_LSM1.
ExpressionAtlasiO15116. baseline and differential.
GenevestigatoriO15116.

Organism-specific databases

HPAiHPA024601.

Interactioni

Subunit structurei

Interacts with SLBP. Interaction with SLBP occurs when histone mRNA is being rapidly degraded during the S phase. LSm subunits form a heteromer with a doughnut shape.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM2Q9Y3333EBI-347619,EBI-347416
LSM3P623103EBI-347619,EBI-348239

Protein-protein interaction databases

BioGridi118104. 33 interactions.
DIPiDIP-31130N.
IntActiO15116. 20 interactions.
MINTiMINT-1036791.
STRINGi9606.ENSP00000310596.

Structurei

3D structure databases

ProteinModelPortaliO15116.
SMRiO15116. Positions 7-123.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiNOG236501.
GeneTreeiENSGT00730000111133.
HOGENOMiHOG000223544.
HOVERGENiHBG027238.
InParanoidiO15116.
KOiK12620.
OMAiFHQTVER.
OrthoDBiEOG7N8ZXQ.
PhylomeDBiO15116.
TreeFamiTF105846.

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.

Sequencei

Sequence statusi: Complete.

O15116-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNYMPGTASL IEDIDKKHLV LLRDGRTLIG FLRSIDQFAN LVLHQTVERI
60 70 80 90 100
HVGKKYGDIP RGIFVVRGEN VVLLGEIDLE KESDTPLQQV SIEEILEEQR
110 120 130
VEQQTKLEAE KLKVQALKDR GLSIPRADTL DEY
Length:133
Mass (Da):15,179
Last modified:January 1, 1998 - v1
Checksum:iFF798CDA9447037A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000177 mRNA. Translation: AAB62189.1.
AJ238094 mRNA. Translation: CAB45865.1.
AK312159 mRNA. Translation: BAG35093.1.
CH471080 Genomic DNA. Translation: EAW63332.1.
BC001767 mRNA. Translation: AAH01767.1.
CCDSiCCDS6103.1.
RefSeqiNP_055277.1. NM_014462.2.
UniGeneiHs.425311.

Genome annotation databases

EnsembliENST00000311351; ENSP00000310596; ENSG00000175324.
GeneIDi27257.
KEGGihsa:27257.
UCSCiuc003xkw.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000177 mRNA. Translation: AAB62189.1.
AJ238094 mRNA. Translation: CAB45865.1.
AK312159 mRNA. Translation: BAG35093.1.
CH471080 Genomic DNA. Translation: EAW63332.1.
BC001767 mRNA. Translation: AAH01767.1.
CCDSiCCDS6103.1.
RefSeqiNP_055277.1. NM_014462.2.
UniGeneiHs.425311.

3D structure databases

ProteinModelPortaliO15116.
SMRiO15116. Positions 7-123.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118104. 33 interactions.
DIPiDIP-31130N.
IntActiO15116. 20 interactions.
MINTiMINT-1036791.
STRINGi9606.ENSP00000310596.

PTM databases

PhosphoSiteiO15116.

Proteomic databases

MaxQBiO15116.
PaxDbiO15116.
PeptideAtlasiO15116.
PRIDEiO15116.

Protocols and materials databases

DNASUi27257.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000311351; ENSP00000310596; ENSG00000175324.
GeneIDi27257.
KEGGihsa:27257.
UCSCiuc003xkw.3. human.

Organism-specific databases

CTDi27257.
GeneCardsiGC08M038020.
HGNCiHGNC:20472. LSM1.
HPAiHPA024601.
MIMi607281. gene.
neXtProtiNX_O15116.
PharmGKBiPA134864226.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG236501.
GeneTreeiENSGT00730000111133.
HOGENOMiHOG000223544.
HOVERGENiHBG027238.
InParanoidiO15116.
KOiK12620.
OMAiFHQTVER.
OrthoDBiEOG7N8ZXQ.
PhylomeDBiO15116.
TreeFamiTF105846.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiLSM1. human.
GeneWikiiLSM1.
GenomeRNAii27257.
NextBioi50202.
PROiO15116.
SOURCEiSearch...

Gene expression databases

BgeeiO15116.
CleanExiHS_LSM1.
ExpressionAtlasiO15116. baseline and differential.
GenevestigatoriO15116.

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. "CaSm: an Sm-like protein that contributes to the transformed state in cancer cells."
    Schweinfest C.W., Graber M.W., Chapman J.M., Papas T.S., Baron P.L., Watson D.K.
    Cancer Res. 57:2961-2965(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "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].
    Tissue: Lymph node.
  3. "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].
    Tissue: Substantia nigra.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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: Eye.
  6. "Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'."
    Mullen T.E., Marzluff W.F.
    Genes Dev. 22:50-65(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HISTONE MRNA DEGRADATION ACTIVITY, INTERACTION WITH SLBP.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiLSM1_HUMAN
AccessioniPrimary (citable) accession number: O15116
Secondary accession number(s): B2R5E6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2002
Last sequence update: January 1, 1998
Last modified: February 4, 2015
This is version 122 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 8
    Human chromosome 8: 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.