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

LSM7 Gene

protein-coding   GIFtS: 55
GCID: GC19M002321

LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)

 Explore 4 diseases affiliated with
LSM7 via our new
 Human Malady Compendium 
Biological research products
for LSM7
    

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

Aliases
LSM7 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae)1 2
YNL147W1 2
U6 SnRNA-Associated Sm-Like Protein LSm72

External Ids:    HGNC: 204701   Entrez Gene: 516902   Ensembl: ENSG000001303327   OMIM: 6072875   UniProtKB: Q9UK453   

Export aliases for LSM7 gene to outside databases

Previous GC identifers: GC19M002384 GC19M002261 GC19M002272 GC19M002092


(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 LSM7:
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: LSM7_HUMAN, Q9UK45
Function: Binds specifically to the 3'-terminal U-tract of U6 snRNA and is probably a component of the spliceosome

Gene Wiki entry for LSM7


(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_000019.9  NC_018930.1  NT_011255.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LSM7 gene promoter:
         GR   USF1   Sp1   USF2   USF-1:USF-2   STAT5A   FOXJ2 (long isoform)   USF-1   FOXJ2   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLSM7 promoter sequence
   Search SABiosciences Chromatin IP Primers for LSM7

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LSM7


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

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

LSM7 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LSM7 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M002321:  view genomic region     (about GC identifiers)

Start:
2,321,520 bp from pter      End:
2,328,615 bp from pter
Size:
7,096 bases      Orientation:
minus 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: LSM7_HUMAN, Q9UK45 (See protein sequence)
Recommended Name: U6 snRNA-associated Sm-like protein LSm7  
Size: 103 amino acids; 11602 Da
Subunit: LSm subunits form a heteromer with a doughnut shape. Also interacts with TACC1
Subcellular location: Nucleus (Potential)

Explore the universe of human proteins at neXtProt for LSM7: NX_Q9UK45

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UK45

  • LSM7 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_057283.1  
    ENSEMBL proteins: 
     ENSP00000466556   ENSP00000467145   ENSP00000252622  
    Reactome Protein details: Q9UK45
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for LSM7

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS--
    GO:0005829cytosol TAS--
    GO:0030529ribonucleoprotein complex IEA--


    LSM7 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

    LSM7 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR001163 Ribonucl_LSM
     IPR006649 Ribonucl_LSM_euk/arc
     IPR010920 LSM_dom
     IPR017132 U6_snRNA_Lsm7

    Graphical View of Domain Structure for InterPro Entry Q9UK45

    ProtoNet protein and cluster: Q9UK45

    2 Blocks protein families:
    IPB001163 Small nuclear ribonucleoprotein (Sm protein)
    IPB010920 Like-Sm ribonucleoprotein-related


    UniProtKB/Swiss-Prot: LSM7_HUMAN, Q9UK45
    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: LSM7_HUMAN, Q9UK45
    Function: Binds specifically to the 3'-terminal U-tract of U6 snRNA and is probably a component of the spliceosome

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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:0005515protein binding IPI--
    GO:0017070U6 snRNA binding NAS10523320


    LSM7 for ontologies           About GeneDecksing


    5 GenomeRNAi human phenotypes for LSM7:
     Decreased homologous recombina  Decreased viability of wild-ty  Decreased viability with pacli  Increased circadian period len 
     Increased gamma-H2AX phosphory 


    (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
    3mRNA Splicing - Major Pathway
    mRNA processing0.48
    Spliceosome0.31
    4Generic Transcription Pathway
    Gene Expression0.46

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    1 BioSystems Pathway for LSM7 
        mRNA processing

    5        Reactome Pathways for LSM7
        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 LSM7):
        RNA degradation
    Spliceosome


    LSM7 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LSM7

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

    5/98 Interacting proteins for LSM7 (Q9UK451, 2, 3 ENSP000002526224) via UniProtKB, MINT, STRING, and/or I2D (see all 98)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    LSM2Q9Y3331, 2, 3, ENSP000003648134EBI-348372,EBI-347416 MINT-62690 MINT-62766 MINT-62592 MINT-8336188 I2D: score=6 STRING: ENSP00000364813
    LSM3P623101, 2, 3, ENSP000003021604EBI-348372,EBI-348239 MINT-8336232 I2D: score=5 STRING: ENSP00000302160
    LSM4Q9Y4Z01, 2, 3, ENSP000002528164EBI-348372,EBI-372521 MINT-8336298 I2D: score=3 STRING: ENSP00000252816
    LSM5Q9Y4Y91, 2, 3, ENSP000004107584EBI-348372,EBI-373007 MINT-8336342 I2D: score=6 STRING: ENSP00000410758
    LSM6P623121, 2, 3, ENSP000002965814EBI-348372,EBI-373310 MINT-8336353 I2D: score=4 STRING: ENSP00000296581
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000288nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS--
    GO:0000398mRNA splicing, via spliceosome NAS--
    GO:0010467gene expression TAS--
    GO:0016070RNA metabolic process TAS--
    GO:0016071mRNA metabolic process TAS--


    LSM7 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 LSM7
    Search CenterWatch for drugs/clinical trials and news about LSM7 

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 LSM7 gene: 
    NM_016199.2  

    Unigene Cluster for LSM7:

    LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)
    Hs.512610  [show with all ESTs]
    Unigene Representative Sequence: AK127573
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000591515 ENST00000589532 ENST00000585395 ENST00000587502 ENST00000585409
    ENST00000252622(uc002lvp.4) ENST00000591745

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    Additional cDNA sequence: 

    AF182293.1 AK127573.1 BC018621.1 

    9 DOTS entries:

    DT.446022  DT.100768058  DT.121414335  DT.91749168  DT.99997695  DT.121414515  DT.121414562  DT.95268954 
    DT.99979042 

    24/164 AceView cDNA sequences (see all 164):

    AA382416 BE644879 BM991504 AA588197 AA358257 BM546845 BM790300 AI081256 
    BM473112 AA481033 AA595320 AI620598 BM023323 BX279582 BU146987 AA722938 
    BC018621 BM663115 BU856494 BQ548745 BU728481 AI369407 AA609823 AI097314 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for LSM7    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c
    SP1:                          -     -                           
    SP2:                          -     -                           
    SP3:                                -                           
    SP4:                          -     -                           
    SP5:                                                            


    ECgene alternative splicing isoforms for LSM7

    (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

    LSM7 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GAGGCCATCC

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

    About this image
    See LSM7 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LSM7

    SOURCE GeneReport for Unigene cluster: Hs.512610
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    In Situ
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    (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 LSM7 gene from 8/30 species (see all 30)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lsm71 , 5 LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)1, 5 87.58(n)1
    98.04(a)1
      10 (39.72 cM)5
    660941  NM_025349.21  NP_079625.11 
     808528255 
    chicken
    (Gallus gallus)
    Aves LSM71 LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) 78.43(n)
    97.06(a)
      420055  NM_001006337.1  NP_001006337.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufj64g012 wufj64g01 80.53(n)   336340  BC055642.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta LSm71 CG13277-PA 70.1(n)
    77.32(a)
      35003  NM_135963.3  NP_609807.1 
    worm
    (Caenorhabditis elegans)
    Secernentea lsm-71 Protein LSM-7 56.33(n)
    57(a)
      177988  NM_069633.3  NP_502034.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes LSM7(YNL147W)4
    LSM71
    Lsm (Like Sm) protein; part of heteroheptameric complexes more4
    Lsm7p1
    49.81(n)1
    49.44(a)1
      14(350940-351383)4
    8555751, 4  NP_014252.21, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G038701 U6 snRNA-associated Sm-like protein LSm7 60.07(n)
    57.14(a)
      814913  NM_126432.3  NP_178480.1 
    rice
    (Oryza sativa)
    Liliopsida Os08g01777001 hypothetical protein 61.48(n)
    56.67(a)
      4344803  NM_001067659.1  NP_001061124.1 


    ENSEMBL Gene Tree for LSM7 (if available)
    TreeFam Gene Tree for LSM7 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/200 NCBI SNPs in LSM7 are shown (see all 200    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs104137791,2
    C--2321067(+) GCCTCT/CTGATG 1 -- int12Minor allele frequency- C:0.00NA 4
    rs1477437311,2
    --2321073(+) TGATGA/CACCCC 1 -- int10--------
    rs1150008861,2
    F,--2321076(+) TGCACC/TCCGGC 1 -- int11Minor allele frequency- T:0.06WA 118
    rs1422414291,2
    C,--2321099(+) CAGCC-/TCCTGAT
    GCACCCCAGG
    TCCTG
    1 -- int10--------
    rs286738591,2
    C,,--2321114(+) ACCCCA/GGCTCC 1 -- int10--------
    rs287330431,2
    --2321116(+) CCCGGC/GTCCTG 1 -- int10--------
    rs729874531,2
    C,F,--2321148(+) ACCCAG/TCTCCT 1 -- int15Minor allele frequency- T:0.19CSA WA NA EA 362
    rs1498185811,2
    --2321197(+) GCACCC/TCGGCT 1 -- int10--------
    rs729874551,2
    C,--2321198(+) CACCCC/TGGCTC 1 -- int15Minor allele frequency- T:0.19CSA WA NA EA 361
    rs285571901,2
    --2321208(+) CCTGAC/TGCACC 1 -- int10--------

    HapMap Linkage Disequilibrium report for LSM7 (2321520 - 2328615 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for LSM7
         1 CNV: 5068

    SABiosciences Cancer Mutation PCR Assays
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    (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

    LSM7 for disorders           About GeneDecksing

    OMIM gene information: 607287    OMIM disorders: --

    4 diseases for LSM7:    About MalaCards
    spinal muscular atrophy    muscular atrophy    breast cancer    malaria


    Export disorders for LSM7 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)
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    PubMed articles for LSM7 gene, integrated from 9 sources (see all 19):
    (articles sorted by number of sources associating them with LSM7)
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    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. (PubMed id 10523320)1, 2, 3 Achsel T....Luhrmann R. (1999)
    2. Carcinogenesis and translational controls: TACC1 is down-regulated in human cancers and associates with mRNA regulators. (PubMed id 12165861)1, 2, 9 Conte N.... Birnbaum D. (2002)
    3. 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)
    4. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (2004)
    5. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. (PubMed id 12515382)1, 3 Ingelfinger D....Achsel T. (2002)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    9. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    10. Defining the human deubiquitinating enzyme interactio n landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 51690 HGNC: 20470 AceView: LSM7 Ensembl:ENSG00000130332 euGenes: HUgn51690
    ECgene: LSM7 Kegg: 51690 H-InvDB: LSM7

    (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 LSM7 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 LSM7 gene:
    Search GeneIP for patents involving LSM7

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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