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] See more...

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
  • U6 SnRNA-Associated Sm-Like Protein LSm2 3 4
  • SnRNP Core Sm-Like Protein Sm-X5 3 4
  • Protein G7b 3 4
  • C6orf28 3 4
  • YBL026W 2 3
  • 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
  • Chromosome 6 Open Reading Frame 28 2
  • SnRNP 3
  • LSM2 5
  • G7b 2

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
  • GC06M032109
  • GC06M032172
  • GC06M032222
  • GC06M032380
  • GC06M031800
  • GC06M031834
  • GC06M031880
  • GC06M031916
  • GC06M031960
  • GC06M031997
  • GC06M032049

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 Mixed Connective Tissue Disease and Spinal Muscular Atrophy. Among its related pathways are mRNA Splicing - Minor Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include Ral GTPase binding.

UniProtKB/Swiss-Prot Summary for LSM2 Gene

  • Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).

Gene Wiki entry for LSM2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LSM2 Gene

Genomics for LSM2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LSM2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LSM2

Top Transcription factor binding sites by QIAGEN in the LSM2 gene promoter:
  • ATF
  • CP2
  • Max1
  • MyoD
  • NF-kappaB
  • NF-kappaB1
  • PPAR-alpha
  • STAT3

Genomic Locations for LSM2 Gene

Genomic Locations for LSM2 Gene
chr6:31,797,396-31,806,966
(GRCh38/hg38)
Size:
9,571 bases
Orientation:
Minus strand
chr6:31,765,173-31,774,761
(GRCh37/hg19)
Size:
9,589 bases
Orientation:
Minus strand

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:
    • Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:11991638, PubMed:28781166). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:10523320, PubMed:28781166, PubMed:26912367). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome (PubMed:10523320, PubMed:26912367, PubMed:28781166).

    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

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

Protein Domains for LSM2 Gene

InterPro:
Blocks:
  • Small nuclear ribonucleoprotein (Sm protein)
  • Like-Sm ribonucleoprotein-related, core
ProtoNet:

Suggested Antigen Peptide Sequences for LSM2 Gene

GenScript: Design optimal peptide antigens:
  • snRNP core Sm-like protein Sm-x5 (LSM2_HUMAN)
  • Small nuclear ribonucleotide protein (Q15520_HUMAN)
  • LSM2 protein (Q6FGG1_HUMAN)

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:
Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).

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 IEA,HDA 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

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM2

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
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 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 21873635
GO:0005634 nucleus IEA,IDA 10523320
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA 21873635
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

2 KEGG pathways for LSM2 Gene
1 Cell Signaling Technology pathway for LSM2 Gene

Gene Ontology (GO) - Biological Process for LSM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000244 spliceosomal tri-snRNP complex assembly IDA 10523320
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0006402 mRNA catabolic process IDA 12515382
GO:0008380 RNA splicing IEA --
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

mRNA/cDNA for LSM2 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM2

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

No ASD Table

Relevant External Links for LSM2 Gene

GeneLoc Exon Structure for
LSM2

Expression for LSM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for LSM2 Gene



Protein tissue co-expression partners for LSM2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LSM2

SOURCE GeneReport for Unigene cluster for LSM2 Gene:

Hs.103106

Evidence on tissue expression from TISSUES for LSM2 Gene

  • Nervous system(4.5)
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
Chimpanzee
(Pan troglodytes)
Mammalia LSM2 30 31
  • 100 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LSM2 31
  • 100 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LSM2 31
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia LSM2 30 31
  • 94.39 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC474849 30
  • 93.68 (n)
Mouse
(Mus musculus)
Mammalia Lsm2 30 17 31
  • 92.2 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lsm2 30
  • 90.43 (n)
Lizard
(Anolis carolinensis)
Reptilia LSM2 31
  • 90 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lsm2 30
  • 79.65 (n)
Str.10738 30
Zebrafish
(Danio rerio)
Actinopterygii smx5 30 31
  • 82.11 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9612 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG10418 30 31
  • 79.49 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005136 30
  • 76.92 (n)
Worm
(Caenorhabditis elegans)
Secernentea gut-2 30 31
  • 69.15 (n)
OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFR182C 30
  • 60.7 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM2 30 31 33
  • 58.6 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F09207g 30
  • 56.14 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT1G03330 30
  • 67.41 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2643 30
Soybean
(Glycine max)
eudicotyledons Gma.2161 30
Rice
(Oryza sativa)
Liliopsida Os08g0154700 30
  • 69.63 (n)
Os.10458 30
Barley
(Hordeum vulgare)
Liliopsida Hv.6066 30
Wheat
(Triticum aestivum)
Liliopsida Ta.6511 30
Bread mold
(Neurospora crassa)
Ascomycetes NCU07382 30
  • 59.92 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm2 30
  • 56.84 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4351 30
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 Squirt (Ciona savignyi)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LSM2: view image

Paralogs for LSM2 Gene

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

  • LSM2_HUMAN

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

Additional dbSNP identifiers (rs#s) for LSM2 Gene

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

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

Variation tolerance for LSM2 Gene

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

Additional Variant Information for LSM2 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LSM2 Gene

Disorders for LSM2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
mixed connective tissue disease
  • connective tissue disease overlap syndrome
spinal muscular atrophy
  • progressive muscular atrophy
connective tissue disease
  • connective tissue 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

Additional Disease Information for LSM2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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
  2. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  3. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4
  4. 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 41
  5. 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 41

Products for LSM2 Gene