Human Gene LSM2 (ENST00000375661.6_7) from GENCODE V47lift37
  Description: LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated (from RefSeq NM_021177.5)
Gencode Transcript: ENST00000375661.6_7
Gencode Gene: ENSG00000204392.11_9
Transcript (Including UTRs)
   Position: hg19 chr6:31,765,173-31,774,743 Size: 9,571 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:31,765,534-31,774,534 Size: 9,001 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:31,765,173-31,774,743)mRNA (may differ from genome)Protein (95 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LSM2_HUMAN
DESCRIPTION: RecName: Full=U6 snRNA-associated Sm-like protein LSm2; AltName: Full=Protein G7b; AltName: Full=Small nuclear ribonuclear protein D homolog; AltName: Full=snRNP core Sm-like protein Sm-x5;
FUNCTION: Binds specifically to the 3'-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.
SUBUNIT: Identified in the spliceosome C complex. LSm subunits form a heteromer with a doughnut shape.
INTERACTION: O15116:LSM1; NbExp=3; IntAct=EBI-347416, EBI-347619; P62310:LSM3; NbExp=8; IntAct=EBI-347416, EBI-348239; Q9UK45:LSM7; NbExp=4; IntAct=EBI-347416, EBI-348372; O95777:NAA38; NbExp=5; IntAct=EBI-347416, EBI-347779; Q9H9D4:ZNF408; NbExp=4; IntAct=EBI-347416, EBI-347633;
SUBCELLULAR LOCATION: Nucleus (Potential).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the snRNP Sm proteins family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LSM2
Diseases sorted by gene-association score: spinal muscular atrophy (4), rheumatic disease (3), collagen disease (1), retinitis pigmentosa (0)

-  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: 62.67 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1017.55 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 -76.40209-0.366 Picture PostScript Text
3' UTR -124.90361-0.346 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
IPR016654 - U6_snRNA_Lsm2

Pfam Domains:
PF01423 - LSM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

ModBase Predicted Comparative 3D Structure on Q9Y333
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 orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0017070 U6 snRNA binding
GO:0017160 Ral GTPase binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005688 U6 snRNP
GO:0005829 cytosol
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071011 precatalytic spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:1990726 Lsm1-7-Pat1 complex


-  Descriptions from all associated GenBank mRNAs
  AF182288 - Homo sapiens U6 snRNA-associated Sm-like protein LSm2 mRNA, complete cds.
BC009192 - Homo sapiens LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:15227 IMAGE:3842537), complete cds.
AF136977 - Homo sapiens snRNP core SM-like protein SM-x5 mRNA, complete cds.
AJ245416 - Homo sapiens mRNA for G7b protein (G7b gene, located in the class III region of the major histocompatibility complex.
JD375207 - Sequence 356231 from Patent EP1572962.
JD245888 - Sequence 226912 from Patent EP1572962.
AF196468 - Homo sapiens SMX5-like protein mRNA, complete cds.
JD481070 - Sequence 462094 from Patent EP1572962.
JD390261 - Sequence 371285 from Patent EP1572962.
JD468782 - Sequence 449806 from Patent EP1572962.
CR542146 - Homo sapiens full open reading frame cDNA clone RZPDo834F0523D for gene LSM2, LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae); complete cds, incl. stopcodon.
KJ894459 - Synthetic construct Homo sapiens clone ccsbBroadEn_03853 LSM2 gene, encodes complete protein.
DQ892903 - Synthetic construct clone IMAGE:100005533; FLH195258.01X; RZPDo839A06152D LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) (LSM2) gene, encodes complete protein.
DQ896539 - Synthetic construct Homo sapiens clone IMAGE:100010999; FLH195254.01L; RZPDo839A06151D LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) (LSM2) gene, encodes complete protein.
AB464333 - Synthetic construct DNA, clone: pF1KB6731, Homo sapiens LSM2 gene for U6 snRNA-associated Sm-like protein LSm2, without stop codon, in Flexi system.
CR542157 - Homo sapiens full open reading frame cDNA clone RZPDo834D0124D for gene LSM2, LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae); complete cds, without stopcodon.
JD258540 - Sequence 239564 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y333 (Reactome details) participates in the following event(s):

R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-429978 Lsm1-7 Complex binds deadenylated mRNA
R-HSA-429845 5' to 3' exoribonuclease hydrolyzes decapped mRNA
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-72172 mRNA Splicing
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: C6orf28, ENST00000375661.1, ENST00000375661.2, ENST00000375661.3, ENST00000375661.4, ENST00000375661.5, G7B, LSM2_HUMAN, NM_021177, Q6FGG1, Q9Y333, uc318mkr.1, uc318mkr.2
UCSC ID: ENST00000375661.6_7
RefSeq Accession: NM_021177.5
Protein: Q9Y333 (aka LSM2_HUMAN)

-  Gene Model Information
  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.