Human Gene LSM1 (uc003xkw.3) Description and Page Index
  Description: Homo sapiens LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) (LSM1), transcript variant 1, mRNA.
RefSeq Summary (NM_014462): This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011].
Transcript (Including UTRs)
   Position: hg19 chr8:38,020,839-38,034,248 Size: 13,410 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr8:38,021,188-38,033,838 Size: 12,651 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:38,020,839-38,034,248)mRNA (may differ from genome)Protein (133 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LSM1_HUMAN
DESCRIPTION: RecName: Full=U6 snRNA-associated Sm-like protein LSm1; AltName: Full=Cancer-associated Sm-like; AltName: Full=Small nuclear ribonuclear CaSm;
FUNCTION: Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3'-terminal U-tract of U6 snRNA.
SUBUNIT: 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.
INTERACTION: Q9Y333:LSM2; NbExp=3; IntAct=EBI-347619, EBI-347416; P62310:LSM3; NbExp=3; IntAct=EBI-347619, EBI-348239;
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Has elevated expression in pancreatic cancer and in several cancer-derived cell lines.
SIMILARITY: Belongs to the snRNP Sm proteins family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LSM1
CDC HuGE Published Literature: LSM1
Positive Disease Associations: Schizophrenia
Related Studies:
  1. Schizophrenia
    Yongyong Shi et al. Nature genetics 2011, Common variants on 8p12 and 1q24.2 confer risk of schizophrenia., Nature genetics. [PubMed 22037555]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.15 RPKM in Cells - Transformed fibroblasts
Total median expression: 1135.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -173.70410-0.424 Picture PostScript Text
3' UTR -81.27349-0.233 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010920 - LSM_dom
IPR001163 - Ribonucl_LSM
IPR006649 - Ribonucl_LSM_euk/arc

Pfam Domains:
PF01423 - LSM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

ModBase Predicted Comparative 3D Structure on O15116
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000339 RNA cap binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0036002 pre-mRNA binding

Biological Process:
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
GO:0000375 RNA splicing, via transesterification reactions
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0019827 stem cell population maintenance
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045665 negative regulation of neuron differentiation
GO:0071044 histone mRNA catabolic process

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005845 mRNA cap binding complex
GO:0030424 axon
GO:0030425 dendrite
GO:0043025 neuronal cell body
GO:1990124 messenger ribonucleoprotein complex
GO:1990726 Lsm1-7-Pat1 complex


-  Descriptions from all associated GenBank mRNAs
  BC001767 - Homo sapiens LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:1352 IMAGE:3353833), complete cds.
AJ238094 - Homo sapiens mRNA for Lsm1 protein.
LF384351 - JP 2014500723-A/191854: Polycomb-Associated Non-Coding RNAs.
AF000177 - Homo sapiens Sm-like protein CaSm (CaSm) mRNA, complete cds.
JD274774 - Sequence 255798 from Patent EP1572962.
JD162622 - Sequence 143646 from Patent EP1572962.
JD174230 - Sequence 155254 from Patent EP1572962.
JD131531 - Sequence 112555 from Patent EP1572962.
AK312159 - Homo sapiens cDNA, FLJ92445, Homo sapiens LSM1 homolog, U6 small nuclear RNA associated (S.cerevisiae) (LSM1), mRNA.
KJ893622 - Synthetic construct Homo sapiens clone ccsbBroadEn_03016 LSM1 gene, encodes complete protein.
AB527991 - Synthetic construct DNA, clone: pF1KB6714, Homo sapiens LSM1 gene for U6 snRNA-associated Sm-like protein LSm1, without stop codon, in Flexi system.
KU178606 - Homo sapiens LSM1-like protein U6 small nuclear RNA associated isoform 1 (LSM1) mRNA, partial cds.
KU178607 - Homo sapiens LSM1-like protein U6 small nuclear RNA associated isoform 3 (LSM1) mRNA, complete cds, alternatively spliced.
AF147348 - Homo sapiens full length insert cDNA clone YB39E01.
LF371812 - JP 2014500723-A/179315: Polycomb-Associated Non-Coding RNAs.
LF371809 - JP 2014500723-A/179312: Polycomb-Associated Non-Coding RNAs.
JD466124 - Sequence 447148 from Patent EP1572962.
JD462096 - Sequence 443120 from Patent EP1572962.
JD138907 - Sequence 119931 from Patent EP1572962.
LF371808 - JP 2014500723-A/179311: Polycomb-Associated Non-Coding RNAs.
MA619928 - JP 2018138019-A/191854: Polycomb-Associated Non-Coding RNAs.
MA607389 - JP 2018138019-A/179315: Polycomb-Associated Non-Coding RNAs.
MA607386 - JP 2018138019-A/179312: Polycomb-Associated Non-Coding RNAs.
MA607385 - JP 2018138019-A/179311: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein O15116 (Reactome details) participates in the following event(s):

R-HSA-429978 Lsm1-7 Complex binds deadenylated mRNA
R-HSA-429845 5' to 3' exoribonuclease hydrolyzes decapped mRNA
R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5E6, CASM, LSM1_HUMAN, NM_014462, NP_055277, O15116
UCSC ID: uc003xkw.3
RefSeq Accession: NM_014462
Protein: O15116 (aka LSM1_HUMAN)
CCDS: CCDS6103.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014462.2
exon count: 4CDS single in 3' UTR: no RNA size: 1161
ORF size: 402CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 601.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.