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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LSM3 Gene

protein-coding   GIFtS: 56
GCID: GC03P014219

LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)

 Explore 3 diseases affiliated with
LSM3 via our new
 Human Malady Compendium 
Biological research products
for LSM3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
LSM3 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae)1 2
SMX41 2
USS21 2
YLR438C1 2
U6 SnRNA-Associated Sm-Like Protein LSm32

External Ids:    HGNC: 178741   Entrez Gene: 272582   Ensembl: ENSG000001708607   OMIM: 6072835   UniProtKB: P623103   

Export aliases for LSM3 gene to outside databases

Previous GC identifers: GC03P014149 GC03P014195 GC03P014155


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for LSM3:
Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see
SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker
of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in
tri-snRNP particles, which are important for pre-mRNA splicing.(supplied by OMIM, Apr 2004)

UniProtKB/Swiss-Prot: LSM3_HUMAN, P62310
Function: Binds specifically to the 3'-terminal U-tract of U6 snRNA

Gene Wiki entry for LSM3


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NC_018914.1  NT_022517.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LSM3 gene promoter:
         Nkx3-1   SRF   Nkx3-1 v4   Brachyury   SRF (504 AA)   p300   LUN-1   Nkx3-1 v1   Nkx3-1 v2   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLSM3 promoter sequence
   Search SABiosciences Chromatin IP Primers for LSM3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LSM3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p25.1   Ensembl cytogenetic band:  3p25.1   HGNC cytogenetic band: 3p25.1

LSM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LSM3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P014219:  view genomic region     (about GC identifiers)

Start:
14,219,858 bp from pter      End:
14,242,619 bp from pter
Size:
22,762 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: LSM3_HUMAN, P62310 (See protein sequence)
Recommended Name: U6 snRNA-associated Sm-like protein LSm3  
Size: 102 amino acids; 11845 Da
Subunit: LSm subunits form a heteromer with a doughnut shape. Identified in the spliceosome C complex
Subcellular location: Nucleus (Potential)
Secondary accessions: Q6IAH0 Q9Y4Z1

Explore the universe of human proteins at neXtProt for LSM3: NX_P62310

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P62310

  • LSM3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055278.1  
    ENSEMBL proteins: 
     ENSP00000302160  
    Reactome Protein details: P62310
    Human Recombinant Protein Products: 
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    ProSpec Recombinant Protein for LSM3
    Uscn Proteins for LSM3

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS10369684
    GO:0005829cytosol TAS--
    GO:0071013catalytic step 2 spliceosome IDA11991638


    LSM3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    LSM3 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR001163 Ribonucl_LSM
     IPR006649 Ribonucl_LSM_euk/arc
     IPR010920 LSM_dom

    Graphical View of Domain Structure for InterPro Entry P62310

    ProtoNet protein and cluster: P62310

    1 Blocks protein family: IPB010920 Like-Sm ribonucleoprotein-related

    UniProtKB/Swiss-Prot: LSM3_HUMAN, P62310
    Similarity: Belongs to the snRNP Sm proteins family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: LSM3_HUMAN, P62310
    Function: Binds specifically to the 3'-terminal U-tract of U6 snRNA

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    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IEA--
    GO:0005515protein binding IPI--


    LSM3 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for LSM3:
     Decreased p24 protein expressi  Large nuclei  Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Deadenylation-dependent mRNA decay
    Deadenylation-dependent mRNA decay1.00
    mRNA Decay by 5' to 3' Exoribonuclease0.31
    RNA degradation0.50
    2Metabolism of mRNA
    Metabolism of mRNA1.00
    Metabolism of RNA0.92
    3Generic Transcription Pathway
    Gene Expression0.46
    4mRNA Splicing - Major Pathway
    Spliceosome0.31

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    5        Reactome Pathways for LSM3
        Deadenylation-dependent mRNA decay
    Metabolism of RNA
    Metabolism of mRNA
    Gene Expression
    mRNA Decay by 5' to 3' Exoribonuclease


    2         Kegg Pathways  (Kegg details for LSM3):
        RNA degradation
    Spliceosome


    LSM3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LSM3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/117 Interacting proteins for LSM3 (P623101, 2, 3 ENSP000003021604) via UniProtKB, MINT, STRING, and/or I2D (see all 117)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    LSM2Q9Y3331, 2, 3, ENSP000003648134EBI-348239,EBI-347416 MINT-62591 MINT-8336166 MINT-62765 MINT-68452 MINT-63961 MINT-62689 I2D: score=9 STRING: ENSP00000364813
    LSM10Q969L41, 2, 3, ENSP000003193414EBI-348239,EBI-373268 MINT-68460 I2D: score=6 STRING: ENSP00000319341
    LSM7Q9UK451, 2, 3, ENSP000002526224EBI-348239,EBI-348372 MINT-8336232 I2D: score=5 STRING: ENSP00000252622
    GDF9O603832, 3MINT-63958 I2D: score=5 
    UTP14AQ9BVJ62, 3MINT-63960 I2D: score=5 
    About this table

    Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000288nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS--
    GO:0000398mRNA splicing, via spliceosome IC11991638
    GO:0006397mRNA processing TAS10369684
    GO:0010467gene expression TAS--
    GO:0016070RNA metabolic process TAS--


    LSM3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LSM3
    Search CenterWatch for drugs/clinical trials and news about LSM3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for LSM3 gene: 
    NM_014463.2  

    Unigene Cluster for LSM3:

    LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)
    Hs.111632  [show with all ESTs]
    Unigene Representative Sequence: BG329333
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000306024(uc003byn.3)

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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LSM3
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LSM3

    Additional cDNA sequence: 

    AF182289.1 AF182418.1 AJ238095.1 AK312189.1 BC007055.1 CR457185.1 

    14 DOTS entries:

    DT.100821302  DT.120920058  DT.100799074  DT.316970  DT.92328070  DT.121011972  DT.91991003  DT.95193911 
    DT.100046091  DT.100658480  DT.100718286  DT.91947897  DT.91989288  DT.99933766 

    24/270 AceView cDNA sequences (see all 270):

    AI953296 BM512021 AI140807 BM543362 BX115936 AA421213 AW959851 CA942843 
    BM746849 BI492640 BM828185 BE621525 CB109603 AI348058 N66147 BM821156 
    BM712300 AA629177 AI523164 AI219040 BF094578 AI167383 CK905723 BX096371 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LSM3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTTATGATCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See LSM3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LSM3

    SOURCE GeneReport for Unigene cluster: Hs.111632
        SABiosciences Custom PCR Arrays for LSM3
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    In Situ
    Assay Products:
     

     
    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for LSM3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for LSM3 gene from 9/36 species (see all 36)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lsm31 , 5 LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)1, 5 90.85(n)1
    100(a)1
      6 (40.58 cM)5
    676781  NM_026309.21  NP_080585.11 
     915159285 
    chicken
    (Gallus gallus)
    Aves LSM31 LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) 84.31(n)
    99.02(a)
      416040  XM_414380.2  XP_414380.1 
    lizard
    (Anolis carolinensis)
    Reptilia LSM36
    --
    99(a)
    1 ↔ 1
    2(169455727-169460685)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.60802 Xenopus laevis transcribed sequence with strong similarity more 79.87(n)    48036382 
    zebrafish
    (Danio rerio)
    Actinopterygii cldng2 claudin g 79.75(n)   81586  BC044441.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta LSm31 CG31184-PA 66.34(n)
    77.45(a)
      42842  NM_001170236.2  NP_001163707.1 
    worm
    (Caenorhabditis elegans)
    Secernentea lsm-31 Protein LSM-3 63.33(n)
    71(a)
      178303  NM_070178.3  NP_502579.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G768601 U6 snRNA-associated Sm-like protein LSm3 70.08(n)
    81.82(a)
      844021  NM_106337.2  NP_177812.1 
    rice
    (Oryza sativa)
    Liliopsida Os.89932 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 76.82(n)    AK099337.1 


    ENSEMBL Gene Tree for LSM3 (if available)
    TreeFam Gene Tree for LSM3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LSM3 gene
    1 SIMAP similar gene for LSM3 using alignment to 1 protein entry:     LSM3_HUMAN:
    SNRPD2

    LSM3 for paralogs           About GeneDecksing


    5 Pseudogenes.org Pseudogenes for LSM3
    PGOHUM00000239897 PGOHUM00000249176 PGOHUM00000237099 PGOHUM00000240121 PGOHUM00000246090


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/298 NCBI SNPs in LSM3 are shown (see all 298    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1155525661,2
    F,--14222180(+) CAGAAA/GGAAGG 1 -- int11Minor allele frequency- G:0.03WA 118
    rs1906320181,2
    --14222288(+) ACCCGA/GACTGC 1 -- int10--------
    rs2008414911,2
    --14222320(+) GCTTG-/CCTTTT 1 -- int10--------
    rs26077381,2
    C--14222321(+) CTTGCC/TTTTTT 1 -- int1 trp31Minor allele frequency- T:0.50WA 2
    rs130924251,2
    C--14222322(+) TTGCCC/TTTTTT 1 -- int1 trp31Minor allele frequency- T:0.50NA 2
    rs1817358201,2
    --14222441(+) CACCTC/TGCCAG 1 -- int10--------
    rs1855553641,2
    --14222442(+) ACCTCA/GCCAGG 1 -- int10--------
    rs1164560171,2
    F,--14222513(+) TGCCCG/AGCTAA 1 -- int11Minor allele frequency- A:0.03NA 120
    rs26077391,2
    C,F,A,H,--14222571(+) TCTTAC/TTCACC 1 -- int129Minor allele frequency- T:0.32NS EA NA WA CSA 2780
    rs1902453121,2
    --14222638(+) CCTCTA/GTTTGG 1 -- int10--------

    HapMap Linkage Disequilibrium report for LSM3 (14219858 - 14242619 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for LSM3
         1 CNV: 48019

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing LSM3
    DNA2.0 Custom Variant and Variant Library Synthesis for LSM3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    LSM3 for disorders           About GeneDecksing

    OMIM gene information: 607283    OMIM disorders: --

    3 diseases for LSM3:    About MalaCards
    spinal muscular atrophy    muscular atrophy    malaria

    Human Genome Epidemiology (HuGE) Navigator: LSM3 (1 document)

    Export disorders for LSM3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LSM3 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with LSM3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. (PubMed id 10369684)1, 2, 3 Salgado-Garrido J.... Seraphin B. (1999)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PubMed id 11991638)1, 2 Jurica M.S.... Moore M.J. (2002)
    4. 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. (PubMed id 10523320)1, 2 Achsel T....Luhrmann R. (1999)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Proliferating cell nuclear antigen (PCNA)-associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyc losome substrate. (PubMed id 21628590)1 Emanuele M.J....Elledge S.J. (2011)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    9. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (PubMed id 17643375)1 Jeronimo C.... Coulombe B. (2007)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 27258 HGNC: 17874 AceView: LSM3 Ensembl:ENSG00000170860 euGenes: HUgn27258
    ECgene: LSM3 Kegg: 27258 H-InvDB: LSM3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for LSM3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LSM3 gene:
    Search GeneIP for patents involving LSM3

    GeneCards and IP:
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