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

SMG6 Gene

protein-coding   GIFtS: 57
GCID: GC17M001963

SMG6 Nonsense Mediated MRNA Decay Factor

(Previous names: chromosome 17 open reading frame 31, smg-6 homolog, nonsense...)
(Previous symbol: C17orf31)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
SMG6 Nonsense Mediated MRNA Decay Factor1 2     SMG-62
C17orf311 2 3     EST1 Telomerase Component Homolog A2
EST1A2 3 5     hSMG5/7a2
Ever Shorter Telomeres 1A2 3     Smg-6 Homolog, Nonsense Mediated MRNA Decay Factor2
Telomerase Subunit EST1A2 3     Telomerase-Binding Protein EST1A2
EST1-Like Protein A2 3     EC 3.1.-.-3
KIAA07323 5     hSmg5/7a3
Chromosome 17 Open Reading Frame 311     Smg-6 Homolog3
EST1 Telomerase Component Homolog A (S. Cerevisiae)1     EC 3.1.138
Smg-6 Homolog, Nonsense Mediated MRNA Decay Factor (C. Elegans)1     EC 3.1.2.158

External Ids:    HGNC: 178091   Entrez Gene: 232932   Ensembl: ENSG000000703667   OMIM: 6109635   UniProtKB: Q86US83   

Export aliases for SMG6 gene to outside databases

Previous GC identifers: GC17M001910 GC17M001916 GC17M001920 GC17M001924 GC17M001926 GC17M001929


(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 SMG6 Gene:
This gene encodes a protein which is part of the telomerase ribonucleoprotein complex and binds single-stranded
DNA found at the telomeres, but the product of this gene also participates in the nonsense-mediated mRNA decay
(NMD) pathway. The encoded protein contains two binding sites for components of the exon junction complex (EJC);
interaction between the encoded protein and the EJC is necessary for NMD activity. Multiple transcript variants
encoding different isoforms have been found for this gene. (provided by RefSeq, Feb 2012)

GeneCards Summary for SMG6 Gene: 
SMG6 (SMG6 nonsense mediated mRNA decay factor) is a protein-coding gene. Diseases associated with SMG6 include lissencephaly, and gigantism, and among its related super-pathways are Metabolism of RNA and Nonsense Mediated Decay Independent of the Exon Junction Complex. GO annotations related to this gene include endoribonuclease activity and telomeric DNA binding. An important paralog of this gene is SMG5.

UniProtKB/Swiss-Prot: EST1A_HUMAN, Q86US8
Function: Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of
chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to
elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA
persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded
5'-(GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER)
Function: Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation
machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to
protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA),
but not ssDNA or dsRNA

Gene Wiki entry for SMG6 Gene


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NT_010718.16  NC_018928.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SMG6 gene promoter:
         Tal-1beta   C/EBPalpha   GATA-1   E47   CHOP-10   AREB6   MZF-1   Cart-1   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMG6 promoter sequence
   Search SABiosciences Chromatin IP Primers for SMG6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMG6


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

Entrez Gene cytogenetic band: 17p13.3   Ensembl cytogenetic band:  17p13.3   HGNC cytogenetic band: 17p13.3

SMG6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMG6 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M001963:  view genomic region     (about GC identifiers)

Start:
1,963,133 bp from pter      End:
2,207,069 bp from pter
Size:
243,937 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: EST1A_HUMAN, Q86US8 (See protein sequence)
Recommended Name: Telomerase-binding protein EST1A  
Size: 1419 amino acids; 160462 Da
Cofactor: Manganese
Subunit: Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10,
NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC). Interacts with TERT, independently
of the telomerase RNA. Interacts with PP2A catalytic subunits, SMG1, UPF1, UPF2 and UPF3B
Subcellular location: Nucleus, nucleolus. Chromosome, telomere (Probable). Cytoplasm, cytosol. Note=Particularly
enriched in the nucleolus
Sequence caution: Sequence=AAH64916.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAA34452.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
3 PDB 3D structures from and Proteopedia for SMG6:
2DOK (3D)        2HWW (3D)        2HWX (3D)    
Secondary accessions: B7Z874 O94837 Q86VH6 Q9UF60
Alternative splicing: 3 isoforms:  Q86US8-1   Q86US8-2   Q86US8-3   

Explore the universe of human proteins at neXtProt for SMG6: NX_Q86US8

Explore proteomics data for SMG6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q86US8

  • 2 DME Specific Peptides for SMG6 (Q86US8)
     DTTRLEI  QLSSPED 

    SMG6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SMG6 Protein Expression
    REFSEQ proteins (4 alternative transcripts): 
    NP_001243756.1  NP_001243757.1  NP_001269255.1  NP_060045.4  

    ENSEMBL proteins: 
     ENSP00000263073   ENSP00000346977   ENSP00000440283   ENSP00000460273   ENSP00000465793  
     ENSP00000466139   ENSP00000466951   ENSP00000459164   ENSP00000460898   ENSP00000458635  
     ENSP00000460191   ENSP00000460301   ENSP00000443920  
    Reactome Protein details: Q86US8
    Human Recombinant Protein Products for SMG6: 
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    Novus Biologicals SMG6 Lysate
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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SMG6 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000781chromosome, telomeric region IEA--
    GO:0005634nucleus IDA--
    GO:0005697telomerase holoenzyme complex TAS12699629
    GO:0005730nucleolus IDA--
    GO:0005737cytoplasm IDA--

    SMG6 for ontologies           About GeneDecksing



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    Cloud-Clone Corp. CLIAs for SMG6


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    5 InterPro protein domains:
     IPR011990 TPR-like_helical
     IPR002716 PIN_dom
     IPR018834 DNA/RNA-bd_Est1-type
     IPR006596 PINc_nuc-bd
     IPR019458 EST1

    Graphical View of Domain Structure for InterPro Entry Q86US8

    ProtoNet protein and cluster: Q86US8

    1 Blocks protein domain: IPB006596 Nucleotide binding protein

    UniProtKB/Swiss-Prot: EST1A_HUMAN, Q86US8
    Domain: The PINc domain confers endonuclease activity and is expected to bind the catalytic metal ion
    Similarity: Contains 1 PINc domain


    SMG6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: EST1A_HUMAN, Q86US8
    Function: Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of
    chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to
    elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA
    persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded
    5'-(GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER)
    Function: Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation
    machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to
    protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA),
    but not ssDNA or dsRNA

         Enzyme Numbers (IUBMB): EC 3.1.2.152 EC 3.1.-.-1 EC 3.1.132

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004521endoribonuclease activity TAS--
    GO:0005515protein binding IPI12699629
    GO:0042162telomeric DNA binding IDA12699629
    GO:0046872metal ion binding IEA--
         
    SMG6 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SMG6:
     Decreased mitotic index 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Smg6):
     no phenotypic analysis 

    SMG6 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SMG6 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMG6 
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    SwitchGear 3'UTR luciferase reporter plasmidSMG6 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SMG6 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Metabolism of mRNA
    Metabolism of mRNA0.92
    Metabolism of RNA0.92
    2Viral mRNA Translation
    Nonsense-Mediated Decay0.84
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex0.84
    3Generic Transcription Pathway
    Gene Expression0.47
    4mRNA surveillance pathway
    mRNA surveillance pathway
    5Regulation of Telomerase
    Regulation of Telomerase

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for SMG6
        Regulation of Telomerase

    5        Reactome Pathways for SMG6
        Nonsense-Mediated Decay
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex
    Metabolism of RNA
    Metabolism of mRNA
    Gene Expression


    1         Kegg Pathway  (Kegg details for SMG6):
        mRNA surveillance pathway


    SMG6 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMG6

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

    5/82 Interacting proteins for SMG6 (Q86US81, 3 ENSP000002630734) via UniProtKB, MINT, STRING, and/or I2D (see all 82)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UPF1Q92900-21, ENSP000002628034EBI-3232100,EBI-373492 I2D: score=1 STRING: ENSP00000262803
    SMG5Q9UPR33, ENSP000003552614I2D: score=1 STRING: ENSP00000355261
    TERTO147463, ENSP000003095724I2D: score=1 STRING: ENSP00000309572
    NLKQ9UBE83I2D: score=3 
    KBTBD7Q8WVZ93I2D: score=1 
    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:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS16488880
    GO:0000723telomere maintenance IMP12699629
    GO:0006406mRNA export from nucleus TAS16488880
    GO:0010467gene expression TAS--
    GO:0016070RNA metabolic process TAS--

    SMG6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SMG6 (EST1A)

    1 HMDB Compound for SMG6    About this table
    CompoundSynonyms CAS #PubMed Ids
    Manganesemanganese 7439-96-5--

    Search CenterWatch for drugs/clinical trials and news about SMG6 / EST1A

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SMG6 gene (5 alternative transcripts): 
    NM_001170957.1  NM_001256827.1  NM_001256828.1  NM_001282326.1  NM_017575.4  

    Unigene Cluster for SMG6:

    Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)
    Hs.448342  [show with all ESTs]
    Unigene Representative Sequence: AB018275
    18/21 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 21):
    ENST00000574501(uc021tno.1) ENST00000263073(uc002fub.1) ENST00000573166
    ENST00000354901 ENST00000570756 ENST00000576218 ENST00000536871 ENST00000573153
    ENST00000573827 ENST00000575454 ENST00000575338 ENST00000570874 ENST00000572369
    ENST00000575176 ENST00000572205 ENST00000571442 ENST00000570659 ENST00000575663

    miRNA
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    Additional mRNA sequence: 

    AB018275.2 AK074270.1 AK093007.1 AK302964.1 AL080204.1 AL133597.1 AY145883.1 AY168921.1 
    BC064916.1 NR_046385.2 

    14 DOTS entries:

    DT.91729366  DT.101967794  DT.95138038  DT.91964190  DT.100804266  DT.100804262  DT.100697919  DT.100804267 
    DT.100716274  DT.102839574  DT.40233768  DT.75125399  DT.75122748  DT.95306739 

    24/191 AceView cDNA sequences (see all 191):

    BU528586 BX357612 AW170545 AI091741 BQ438085 AL705416 BM703714 BM693685 
    BM272107 CD244675 AA910570 BU527860 AI652673 AW517318 AW196006 AI653849 
    BU859251 AA699953 BM929789 CR602852 AL546613 BQ029478 AI742136 BX092693 

    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

    SMG6 expression in normal human tissues (normalized intensities)      SMG6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCTGACTGC
    SMG6 Expression
    About this image


    SMG6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Heart (Cardiovascular System)
             Atrioventricular Node Cells Atrioventricular Node
     
     Gut Tube (Gastrointestinal Tract)
             Definitive endoderm-like cells ( A scalable, suspension protocol for derivation of...
     
     Umbilical Cord (Extraembryonic Tissues)
     
     Uterus (Reproductive System)

    See SMG6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMG6

    SOURCE GeneReport for Unigene cluster: Hs.448342

    UniProtKB/Swiss-Prot: EST1A_HUMAN, Q86US8
    Tissue specificity: Ubiquitous

        SABiosciences Expression via Pathway-Focused PCR Array including SMG6: 
              Telomeres & Telomerase in human mouse rat

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMG6

    (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 animals.

    Orthologs for SMG6 gene from 7/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smg61 , 5 Smg-6 homolog, nonsense mediated mRNA decay factor more1, 5 88.5(n)1
    90.9(a)1
      11 (45.76 cM)5
    1036771  NM_001002764.11  NP_001002764.11 
     749258235 
    chicken
    (Gallus gallus)
    Aves SMG61 Smg-6 homolog, nonsense mediated mRNA decay factor more 73.17(n)
    72.95(a)
      771628  XM_001234884.2  XP_001234885.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    SMG66
    Uncharacterized protein
    80(a)
    57(a)
    possible ortholog
    1 ↔ 1
    GL344562.1(26450-29114)
    GL343470.1(595707-660163)
    African clawed frog
    (Xenopus laevis)
    Amphibia BQ400176.12   -- 79.02(n)    BQ400176.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003340201 telomerase-binding protein EST1A-like 58.28(n)
    55.97(a)
      100334020  XM_002663611.2  XP_002663657.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta Smg61 CG6369-PA 43.72(n)
    29.5(a)
      42994  NM_143064.1  NP_651321.1 
    worm
    (Caenorhabditis elegans)
    Secernentea smg-66
    Protein SMG-6, isoform a
    18(a)
    1 ↔ 1
    III(2473868-2486626)


    ENSEMBL Gene Tree for SMG6 (if available)
    TreeFam Gene Tree for SMG6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SMG6 gene
    SMG52  SMG72  

    SMG6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/4914 SNPs in SMG6 are shown (see all 4914)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1849330851,2
    C--1963483(+) AGATTG/TGCCCC 4 -- ut31 nc-transcript-variant0--------
    rs1381000551,2
    C--1963592(+) ACCAGC/GTAAAG 4 -- ut31 nc-transcript-variant0--------
    rs1495277901,2
    C--1963596(+) GCTAAA/GGGGGC 4 -- ut31 nc-transcript-variant0--------
    rs1459422901,2
    C--1963744(+) GAGCCA/GAGGGT 4 -- ut31 nc-transcript-variant0--------
    rs1889446821,2
    --1963947(+) GGTGAA/TGGGGG 4 -- ut31 nc-transcript-variant0--------
    rs129465641,2
    C,F--1963961(+) TGAGGA/G/TGAGTC 8 -- ut31 nc-transcript-variantese313NA WA CSA EA 376
    rs9031581,2
    C,F,A,H--1964018(-) TCCCTC/TTCTCC 4 -- ut31 nc-transcript-variantese3 trp330Minor allele frequency- G:0.00EA NA MN NS WA CSA 2683
    rs1922628281,2
    --1964095(+) GTCCAC/TGGGGA 4 -- ut31 nc-transcript-variant0--------
    rs1415308111,2
    --1964247(+) ACTTGC/GGTTCA 4 -- ut31 nc-transcript-variant0--------
    rs10455241,2
    F--1964270(-) TCCCTA/GAGGCC 4 -- ut31 nc-transcript-variantese30--------

    HapMap Linkage Disequilibrium report for SMG6 (1963133 - 2207069 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/21 variations for SMG6 (see all 21):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2715494CNV Deletion23290073
    esv2715491CNV Deletion23290073
    esv2715497CNV Deletion23290073
    esv2715498CNV Deletion23290073
    esv1259463CNV Deletion17803354
    esv2668978CNV Deletion23128226
    esv2715495CNV Deletion23290073
    esv2715500CNV Deletion23290073
    esv2715499CNV Deletion23290073
    esv3071CNV Deletion18987735

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 610963    OMIM disorders: --

    3 diseases for SMG6:    About MalaCards
    lissencephaly    gigantism    schizophrenia


    SMG6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SMG6
    Human Genome Epidemiology (HuGE) Navigator: SMG6 (6 documents)

    Export disorders for SMG6 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 SMG6 gene, integrated from 9 sources (see all 42):
    (articles sorted by number of sources associating them with SMG6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Functional conservation of the telomerase protein Est1p in humans. (PubMed id 12699629)1, 2, 3 Snow B.E....Harrington L. (2003)
    2. A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed. (PubMed id 12676087)1, 2, 3 Reichenbach P....Lingner J. (2003)
    3. Evidence for association between structural variants in lissencephaly-related genes and executive deficits in schizophrenia or bipolar patients from a Spanish isolate population. (PubMed id 19018238)1, 4, 9 Tabares-Seisdedos R....Martinez S. (2008)
    4. Large-scale association analysis identifies 13 new su sceptibility loci for coronary artery disease. (PubMed id 21378990)1, 4 Schunkert H....Samani N.J. (2011)
    5. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    6. SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. (PubMed id 19060897)1, 2 Eberle A.B.... Jensen T.H. (2009)
    7. Genetic variants associated with cardiac structure an d function: a meta-analysis and replication of genome-wide association data. (PubMed id 19584346)1, 4 Vasan R.S....Blankenberg S. (2009)
    8. SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. (PubMed id 18974281)1, 2 Huntzinger E.... Izaurralde E. (2008)
    9. Crystal structure of the PIN domain of human telomerase-associated protein EST1A. (PubMed id 17557331)1, 2 Takeshita D....Tanokura M. (2007)
    10. Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. (PubMed id 17053788)1, 2 Glavan F.... Conti E. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23293 HGNC: 17809 AceView: SMYD4 Ensembl:ENSG00000070366 euGenes: HUgn23293
    ECgene: SMG6 Kegg: 23293 H-InvDB: SMG6

    (According to HUGE)
    About This Section
    HUGE: KIAA0732

    (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 SMG6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SMG6 gene:
    Search GeneIP for patents involving SMG6

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



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