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Aliases for LSM2 Gene

Aliases for LSM2 Gene

  • LSM2 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • Small Nuclear Ribonuclear Protein D Homolog 3 4
  • SnRNP Core Sm-Like Protein Sm-X5 3 4
  • Protein G7b 3 4
  • C6orf28 3 4
  • G7B 3 4
  • LSM2 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM2 U6 Small Nuclear RNA And MRNA Degradation Associated 3
  • LSM2 Homolog, U6 Small Nuclear RNA Associated 3
  • U6 SnRNA-Associated Sm-Like Protein LSm2 3
  • Chromosome 6 Open Reading Frame 28 2
  • YBL026W 3
  • SnRNP 3

External Ids for LSM2 Gene

Previous HGNC Symbols for LSM2 Gene

  • C6orf28

Previous GeneCards Identifiers for LSM2 Gene

  • GC06M031819
  • GC06M031535
  • GC06M031869
  • GC06M031873
  • GC06M031765
  • GC06M031553
  • GC06M031798
  • GC06M031800
  • GC06M031834
  • GC06M031880

Summaries for LSM2 Gene

Entrez Gene Summary for LSM2 Gene

  • 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. Pseudogenes of this gene are located on the short arm of chromosomes 6 and 19. [provided by RefSeq, Nov 2011]

GeneCards Summary for LSM2 Gene

LSM2 (LSM2 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated) is a Protein Coding gene. Diseases associated with LSM2 include Spinal Muscular Atrophy and Rheumatic Disease. Among its related pathways are Translational Control and mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding and Ral GTPase binding.

UniProtKB/Swiss-Prot for LSM2 Gene

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

Gene Wiki entry for LSM2 Gene

Additional gene information for LSM2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM2 Gene

Genomics for LSM2 Gene

Regulatory Elements for LSM2 Gene

Enhancers for LSM2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H031538 1.4 ENCODE dbSUPER 91.7 +265.8 265846 4.9 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF143 SP3 MCM3 PPARGC1A MEF2D ATF6B LSM2 LY6G5B DDX39B MDC1 PPP1R10 NRM DHX16 MSH5 TCF19
GH06H031619 1.4 ENCODE dbSUPER 79.3 +185.8 185757 4 ZFP64 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC MEF2D SSRP1 ZNF610 LSM2 ATF6B GTF2H4 LY6G5B MDC1 PPT2 DDX39B EGFL8 NFKBIL1 DXO
GH06H030907 1.2 ENCODE 90.9 +898.5 898527 2.2 DMAP1 YBX1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A MEF2D MDC1 GTF2H4 TRIM39 LY6G5B LSM2 DDX39B HCG18 PPP1R10 ENSG00000233892 DHX16
GH06H031733 1.9 FANTOM5 ENCODE dbSUPER 56.7 +69.5 69530 8.5 MLX ZFP64 YBX1 FEZF1 DMAP1 YY1 SLC30A9 SP3 NFYC ZC3H11A LY6G5B ATF6B DDX39B LSM2 CSNK2B GPANK1 VARS NFKBIL1 SKIV2L MSH5
GH06H031829 1.4 ENCODE dbSUPER 70.4 -27.2 -27173 9.1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 ZC3H11A MEF2D GLIS1 NBN ATF6B LY6G5B DDX39B LSM2 CSNK2B MSH5 SKIV2L BAG6 VARS GPANK1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LSM2 on UCSC Golden Path with GeneCards custom track

Promoters for LSM2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195602 284 1001 HDGF FOXA2 PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1

Genomic Locations for LSM2 Gene

Genomic Locations for LSM2 Gene
chr6:31,797,392-31,806,984
(GRCh38/hg38)
Size:
9,593 bases
Orientation:
Minus strand
chr6:31,765,173-31,774,761
(GRCh37/hg19)

Genomic View for LSM2 Gene

Genes around LSM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for LSM2 Gene

  • Protein details for LSM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y333-LSM2_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm2
    Protein Accession:
    Q9Y333
    Secondary Accessions:
    • Q6FGG1

    Protein attributes for LSM2 Gene

    Size:
    95 amino acids
    Molecular mass:
    10835 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. LSm subunits form a heteromer with a doughnut shape.

    Three dimensional structures from OCA and Proteopedia for LSM2 Gene

neXtProt entry for LSM2 Gene

Post-translational modifications for LSM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LSM2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LSM2 Gene

Domains & Families for LSM2 Gene

Gene Families for LSM2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for LSM2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y333

UniProtKB/Swiss-Prot:

LSM2_HUMAN :
  • Belongs to the snRNP Sm proteins family.
Family:
  • Belongs to the snRNP Sm proteins family.
genes like me logo Genes that share domains with LSM2: view

Function for LSM2 Gene

Molecular function for LSM2 Gene

UniProtKB/Swiss-Prot Function:
Binds specifically to the 3-terminal U-tract of U6 snRNA. May be involved in pre-mRNA splicing.

Phenotypes From GWAS Catalog for LSM2 Gene

Gene Ontology (GO) - Molecular Function for LSM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA,IDA 22658674
GO:0005515 protein binding IPI 14667819
GO:0017070 U6 snRNA binding NAS 10523320
GO:0017160 Ral GTPase binding IPI 24056301
genes like me logo Genes that share ontologies with LSM2: view
genes like me logo Genes that share phenotypes with LSM2: view

miRNA for LSM2 Gene

miRTarBase miRNAs that target LSM2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LSM2 Gene

Localization for LSM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LSM2 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LSM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA --
genes like me logo Genes that share ontologies with LSM2: view

Pathways & Interactions for LSM2 Gene

genes like me logo Genes that share pathways with LSM2: view

Pathways by source for LSM2 Gene

1 Cell Signaling Technology pathway for LSM2 Gene
1 BioSystems pathway for LSM2 Gene

Gene Ontology (GO) - Biological Process for LSM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
genes like me logo Genes that share ontologies with LSM2: view

No data available for SIGNOR curated interactions for LSM2 Gene

Drugs & Compounds for LSM2 Gene

(7) Drugs for LSM2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for LSM2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LSM2: view

Transcripts for LSM2 Gene

Unigene Clusters for LSM2 Gene

LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LSM2 Gene

No ASD Table

Relevant External Links for LSM2 Gene

GeneLoc Exon Structure for
LSM2
ECgene alternative splicing isoforms for
LSM2

Expression for LSM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LSM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LSM2 Gene

This gene is overexpressed in Tlymphocyte (10.1), Peripheral blood mononuclear cells (9.3), and Nasal epithelium (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LSM2 Gene



Protein tissue co-expression partners for LSM2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LSM2 Gene:

LSM2

SOURCE GeneReport for Unigene cluster for LSM2 Gene:

Hs.103106

Evidence on tissue expression from TISSUES for LSM2 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LSM2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LSM2 Gene

Orthologs for LSM2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM2 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia LSM2 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LSM2 34 33
  • 100 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSM2 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LSM2 34 33
  • 94.39 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LOC474849 33
  • 93.68 (n)
mouse
(Mus musculus)
Mammalia Lsm2 16 34 33
  • 92.2 (n)
rat
(Rattus norvegicus)
Mammalia Lsm2 33
  • 90.43 (n)
lizard
(Anolis carolinensis)
Reptilia LSM2 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm2 33
  • 79.65 (n)
Str.10738 33
zebrafish
(Danio rerio)
Actinopterygii smx5 33 34
  • 82.11 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9612 33
fruit fly
(Drosophila melanogaster)
Insecta CG10418 33 34
  • 79.49 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005136 33
  • 76.92 (n)
worm
(Caenorhabditis elegans)
Secernentea gut-2 33 34
  • 69.15 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR182C 33
  • 60.7 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM2 33 34 36
  • 58.6 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F09207g 33
  • 56.14 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G03330 33
  • 67.41 (n)
soybean
(Glycine max)
eudicotyledons Gma.2161 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2643 33
rice
(Oryza sativa)
Liliopsida Os08g0154700 33
  • 69.63 (n)
Os.10458 33
barley
(Hordeum vulgare)
Liliopsida Hv.6066 33
wheat
(Triticum aestivum)
Liliopsida Ta.6511 33
bread mold
(Neurospora crassa)
Ascomycetes NCU07382 33
  • 59.92 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm2 33
  • 56.84 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4351 33
Species where no ortholog for LSM2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for LSM2 Gene

ENSEMBL:
Gene Tree for LSM2 (if available)
TreeFam:
Gene Tree for LSM2 (if available)

Paralogs for LSM2 Gene

(3) SIMAP similar genes for LSM2 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for LSM2 Gene

genes like me logo Genes that share paralogs with LSM2: view

No data available for Paralogs for LSM2 Gene

Variants for LSM2 Gene

Sequence variations from dbSNP and Humsavar for LSM2 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000456623 -- 31,806,921(+) GCGCG(A/G)CCGAC utr-variant-5-prime
rs1000898675 -- 31,799,328(+) TGAGT(A/G)GCTGT intron-variant
rs1000942439 -- 31,807,759(+) CACGC(A/G)CCTGT upstream-variant-2KB
rs1001422238 -- 31,805,161(+) CTGGG(C/T)TCAAG intron-variant
rs1001533722 -- 31,801,694(+) GGGAG(A/G)CTGAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LSM2 Gene

Variant ID Type Subtype PubMed ID
nsv1126749 CNV deletion 24896259
nsv1112900 CNV deletion 24896259
nsv1073969 CNV deletion 25765185
dgv10404n54 CNV loss 21841781
dgv10403n54 CNV loss 21841781

Variation tolerance for LSM2 Gene

Residual Variation Intolerance Score: 50.7% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LSM2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM2 Gene

Disorders for LSM2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LSM2 Gene - From: Novoseek and GeneCards

Disorder Aliases PubMed IDs
spinal muscular atrophy
  • juvenile spinal muscular atrophy
rheumatic disease
  • collagen diseases
collagen disease
  • collagen disorder
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search LSM2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LSM2

Genetic Association Database (GAD)
LSM2
Human Genome Epidemiology (HuGE) Navigator
LSM2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LSM2
genes like me logo Genes that share disorders with LSM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LSM2 Gene

Publications for LSM2 Gene

  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. (PMID: 10523320) Achsel T … Lührmann R (The EMBO journal 1999) 2 3 4 60
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 60
  4. Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers. (PMID: 18095154) Walker LC … Spurdle AB (Breast cancer research and treatment 2008) 3 45 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for LSM2 Gene

Sources for LSM2 Gene