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    LSM2 LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [ Homo sapiens ]

    Gene ID: 57819, updated on 19-May-2012
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    Summary

    Official Symbol
    LSM2provided by HGNC
    Official Full Name
    LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)provided by HGNC
    Primary source
    HGNC:13940
    Locus tag
    DAAP-21F2.6
    See related
    Ensembl:ENSG00000204392; HPRD:06282; MIM:607282; Vega:OTTHUMG00000031121
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    G7B; snRNP; C6orf28; YBL026W
    Summary
    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]
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    Genomic context

    Location :
    6p21.3
    Sequence :
    Chromosome: 6; NC_000006.11 (31765173..31774743, complement)
    See LSM2 in Epigenomics, MapViewer

    Chromosome 6 - NC_000006.11Genomic Context describing neighboring genes Neighboring gene von Willebrand factor A domain containing 7 Neighboring gene valyl-tRNA synthetase Neighboring gene heat shock 70kDa protein 1-like Neighboring gene heat shock 70kDa protein 1A

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Danielsen JM, et al. Mol Cell Proteomics, 2011 Mar. PMID 21139048.
    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. Bailey SD, et al. Diabetes Care, 2010 Oct. PMID 20628086.
    3. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Talmud PJ, et al. Am J Hum Genet, 2009 Nov. PMID 19913121.
    4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. Barcellos LF, et al. PLoS Genet, 2009 Oct. PMID 19851445.
    5. Defining the human deubiquitinating enzyme interaction landscape. Sowa ME, et al. Cell, 2009 Jul 23. PMID 19615732.

    See all (29) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    3. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: 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.
    4. LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci
      Title: The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci.
    Submit: New GeneRIF Correction
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    Q9Y333 Q9UKR5 C14orf1    HPRD  PubMed  
    Q9Y333 Q14194 CRMP1    HPRD  PubMed  
    Q9Y333 P31689 DNAJA1    HPRD  PubMed  
    Q9Y333 Q01780 EXOSC10    HPRD  PubMed  
    Q9Y333 P32456 GBP2    HPRD  PubMed  
    Q9Y333 O15116 LSM1    HPRD  PubMed  
    Q9Y333 P62310 LSM3    HPRD  PubMed  
    Q9Y333 Q9Y4Y9 LSM5    HPRD  PubMed  
    Q9Y333 P62312 LSM6    HPRD  PubMed  
    Q9Y333 Q9UK45 LSM7    HPRD  PubMed  
    Q9Y333 O95777 NAA38    HPRD  PubMed  
    Q9Y333 Q96IZ7 RSRC1    HPRD  PubMed  
    Q9Y333 Q16637 SMN2    HPRD  PubMed  
    Q9Y333 P62316 SNRPD2    HPRD  PubMed  
    Q9Y333 P62304 SNRPE    HPRD  PubMed  
    Q9Y333 Q05516 ZBTB16    HPRD  PubMed  
    Q9Y333 Q9H9D4 ZNF408    HPRD  PubMed  
    BioGRID:121778 BioGRID:116332 C14orf1    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:107790 CRMP1    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:116387 DDX20    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:121778 BioGRID:108325 EMD    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:108904 GBP2    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:118104 LSM1    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:118105 LSM3    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:117336 LSM4    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:121778 BioGRID:119678 LSM7    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:121122 MEPCE    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:119679 NAA38    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:114576 PRPF4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:119470 RSRC1    BioGRID  PubMed Two-hybrid 
    BioGRID:121778 BioGRID:115082 SART3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:112490 SMN1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:121778 BioGRID:112497 SUMO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:115283 USP15    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:113221 USP4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:121778 BioGRID:113498 ZBTB16    BioGRID  PubMed Two-hybrid 
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    General gene information

    Markers

    Genotypes

    Homology

    • Homologs of the LSM2 gene: The LSM2 gene is conserved in chimpanzee, , dog, cow, mouse, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, , S.pombe, , N.crassa, A.thaliana, rice, and P.falciparum.
    • Map Viewer (Mouse)

    Pathways from BioSystems

    • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
      Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Lsm 1-7 complex, organism-specific biosystem (from KEGG)
      Lsm 1-7 complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
    • Lsm 2-8 complex, organism-specific biosystem (from KEGG)
      Lsm 2-8 complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
    • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
      Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
    • RNA degradation, organism-specific biosystem (from KEGG)
      RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
    • RNA degradation, conserved biosystem (from KEGG)
      RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
    • Spliceosome, organism-specific biosystem (from KEGG)
      Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
    • Spliceosome, conserved biosystem (from KEGG)
      Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
    • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
      Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
    • mRNA Decay by 5' to 3' Exoribonuclease, organism-specific biosystem (from REACTOME)
      mRNA Decay by 5' to 3' Exoribonuclease, organism-specific biosystemDegradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-...
    • mRNA Splicing, organism-specific biosystem (from REACTOME)
      mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
    • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
      mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
    • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
      mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...
    • mRNA processing, organism-specific biosystem (from WikiPathways)
      mRNA processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    U6 snRNA binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    protein kinase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    RNA metabolic process TAS
    Traceable Author Statement
    more info
    		  
    RNA splicing TAS
    Traceable Author Statement
    more info
    		  
    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
    Traceable Author Statement
    more info
    		  
    gene expression TAS
    Traceable Author Statement
    more info
    		  
    mRNA metabolic process TAS
    Traceable Author Statement
    more info
    		  
    nuclear mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    nuclear mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		  
    nuclear mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    		  
    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
    		  
    nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    nucleus NAS
    Non-traceable Author Statement
    more info
    		  
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    General protein information

    Preferred Names
    U6 snRNA-associated Sm-like protein LSm2
    Names
    U6 snRNA-associated Sm-like protein LSm2
    protein G7b
    snRNP core Sm-like protein Sm-x5
    small nuclear ribonuclear protein D homolog
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    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_021177.4 → NP_067000.1  U6 snRNA-associated Sm-like protein LSm2

      Status: REVIEWED

      Source sequence(s)
      AF136977, AI570628, BP203102, BU189898
      Consensus CDS
      CCDS4722.1
      UniProtKB/TrEMBL
      Q6FGG1
      UniProtKB/Swiss-Prot
      Q9Y333
      Related
      ENSP00000364813, OTTHUMP00000029159, ENST00000375661, OTTHUMT00000076205
      Conserved Domains (1) summary
      cd01725
      Location:2 – 82
      Blast Score: 435
      LSm2; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of ...

    RefSeqs of Annotated Genomes: Build 37.3

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000006.11 Reference GRCh37.p5 Primary Assembly

      Range
      31765173..31774743, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.1 Reference GRCh37.p5 ALT_REF_LOCI_1

      Range
      3079923..3089494, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.2 Reference GRCh37.p5 ALT_REF_LOCI_2

      Range
      3274741..3284314, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.1 Reference GRCh37.p5 ALT_REF_LOCI_3

      Range
      3050755..3060326, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.1 Reference GRCh37.p5 ALT_REF_LOCI_5

      Range
      3144870..3154441, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh37.p5 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.1 Reference GRCh37.p5 ALT_REF_LOCI_6

      Range
      3058818..3068380, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000138.1 Alternate HuRef

      Range
      31551579..31561151, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AF134726.1 AAD21818.1
    genomic AL662834.8 (61267..70840) None
    genomic AL671762.10 (5242..14812) None
    genomic AL929592.8 CAI18462.1
    genomic BA000025.2 BAB63302.1
    genomic CH471081.1 EAX03525.1
      EAX03526.1
    genomic CR759787.4 CAQ10128.1
    genomic CR759915.6 CAQ07255.1
    genomic CR925765.2 CAQ10626.1
    mRNA AF136977.1 AAG49438.1
    mRNA AF182288.1 AAD56226.1
    mRNA AF196468.1 AAG33023.1
    mRNA AI570628.1 None
    mRNA AJ245416.1 CAB52190.1
    mRNA BC009192.2 AAH09192.1
    mRNA BP203102.1 None
    mRNA BU189898.1 None
    mRNA CR542146.1 CAG46943.1
    mRNA CR542157.1 CAG46954.1
    other-genetic DQ892903.2 ABM83829.1
    other-genetic DQ896539.2 ABM87538.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6FGG1 GenPept UniProtKB/TrEMBL:Q6FGG1
    Q9Y333.1 GenPept UniProtKB/Swiss-Prot:Q9Y333
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    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Medical
    Molecular Biology Databases
    Research Materials
    Miscellaneous

      Supplemental Content

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