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SMG1 Gene

protein-coding   GIFtS: 65
GCID: GC16M018816

SMG1 Phosphatidylinositol 3-Kinase-Related Kinase

(Previous names: smg-1 homolog, phosphatidylinositol 3-kinase-related kinase...)
  See SMG1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
SMG1 Phosphatidylinositol 3-Kinase-Related Kinase1 2     Phosphatidylinositol 3-Kinase-Related Kinase1
LIP2 3 5     Smg-1 Homolog, Phosphatidylinositol 3-Kinase-Related Kinase (C. Elegans)1
Lambda-Interacting Protein2 3     PI-3-Kinase-Related Kinase SMG-12
Lambda/Iota Protein Kinase C-Interacting Protein2 3     Serine/Threonine-Protein Kinase SMG12
61E3.42 3     Smg-1 Homolog, Phosphatidylinositol 3-Kinase-Related Kinase2
ATX2 3     SMG-13
EC 2.7.11.13 8     hSMG-13
KIAA04213 5     EC 2.7.118

External Ids:    HGNC: 300451   Entrez Gene: 230492   Ensembl: ENSG000001571067   OMIM: 6070325   UniProtKB: Q96Q153   

Export aliases for SMG1 gene to outside databases

Previous GC identifers: GC16M018309 GC16M018746 GC16M018785 GC16M018726 GC16M017358


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SMG1 Gene:
This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance
complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of
nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their
full-length nature has yet to be determined. (provided by RefSeq, Mar 2013)

GeneCards Summary for SMG1 Gene:
SMG1 (SMG1 phosphatidylinositol 3-kinase-related kinase) is a protein-coding gene. Diseases associated with SMG1 include ullrich congenital muscular dystrophy. GO annotations related to this gene include protein serine/threonine kinase activity and protein kinase activity. An important paralog of this gene is ENSG00000261740.

UniProtKB/Swiss-Prot: SMG1_HUMAN, Q96Q15
Function: Serine/threonine protein kinase involved in both mRNA surveillance and genotoxic stress response
pathways. Recognizes the substrate consensus sequence [ST]-Q. Plays a central role in nonsense-mediated decay
(NMD) of mRNAs containing premature stop codons by phosphorylating UPF1/RENT1. Recruited by release factors to
stalled ribosomes together with SMG8 and SMG9 (forming the SMG1C protein kinase complex), and UPF1 to form the
transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon
junction complex (EJC) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is
believed to activate NMD. Also acts as a genotoxic stress-activated protein kinase that displays some functional
overlap with ATM. Can phosphorylate p53/TP53 and is required for optimal p53/TP53 activation after cellular
exposure to genotoxic stress. Its depletion leads to spontaneous DNA damage and increased sensitivity to ionizing
radiation (IR). May activate PRKCI but not PRKCZ

Gene Wiki entry for SMG1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NT_187260.1  NC_018927.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMG1 gene promoter:
         LHX3b/Lhx3b   AP-2alpha isoform 3   p53   AP-2alpha isoform 2   AREB6   Pax-3   LHX3a/Lhx3a   AP-2alpha isoform 4   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SMG1 promoter sequence
   Search Chromatin IP Primers for SMG1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMG1


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

Entrez Gene cytogenetic band: 16p12.3   Ensembl cytogenetic band:  16p12.3   HGNC cytogenetic band: 16p12.3

SMG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMG1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M018816:  view genomic region     (about GC identifiers)

Start:
18,816,175 bp from pter      End:
18,937,776 bp from pter
Size:
121,602 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMG1_HUMAN, Q96Q15 (See protein sequence)
Recommended Name: Serine/threonine-protein kinase SMG1  
Size: 3661 amino acids; 410501 Da
Cofactor: Manganese
Subunit: Component of the SMG1C complex composed of SMG1, SMG8 and SMG9; the recruitment of SMG8 to SMG1
N-terminus induces a large conformational change in the SMG1 C-terminal head domain containing the catalytic
domain. Component of the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. Interacts with PRKCI. Interacts with TELO2
and TTI1. Interacts with RUVBL1 and RUVBL2. Interacts with UPF2
Miscellaneous: This gene is located in a region of chromosome 16 that contains 2 segmental duplications. Other
genes that are highly related to this exist, but they probably represent pseudogenes
Sequence caution: Sequence=AAA86535.2; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: O43305 Q13284 Q8NFX2 Q96QV0 Q96RW3
Alternative splicing: 4 isoforms:  Q96Q15-1   Q96Q15-2   Q96Q15-3   Q96Q15-4   

Explore the universe of human proteins at neXtProt for SMG1: NX_Q96Q15

Explore proteomics data for SMG1 at MOPED

Post-translational modifications: 

  • Autophosphorylated (Probable)1
  • Ubiquitination2 at Lys529, Lys598, Lys1632
  • Modification sites at PhosphoSitePlus
  • 4 DME Specific Peptides for SMG1 (Q96Q15)
     VLRGCLE  DPLVDWT  TGEVVHID  LPTKTKPKK 


    See SMG1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055907.3  
    ENSEMBL proteins: 
     ENSP00000402515   ENSP00000456259   ENSP00000455861   ENSP00000458558   ENSP00000460854  
     ENSP00000458380   ENSP00000432825   ENSP00000455453   ENSP00000456025   ENSP00000374118  
    Reactome Protein details: Q96Q15

    SMG1 Human Recombinant Protein Products:

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    Novus Biologicals SMG1 Protein
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SMG1

     
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    Cloud-Clone Corp. ELISAs for SMG1
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    Search eBioscience for ELISAs for SMG1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    IUPHAR Guide to PHARMACOLOGY protein family classification: smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)
    SMG1 subfamily

    Selected InterPro protein domains (see all 6):
     IPR011009 Kinase-like_dom
     IPR014009 PIK_FAT
     IPR000403 PI3/4_kinase_cat_dom
     IPR016024 ARM-type_fold
     IPR003152 FATC

    Graphical View of Domain Structure for InterPro Entry Q96Q15

    ProtoNet protein and cluster: Q96Q15

    3 Blocks protein domains:
    IPB000357 HEAT repeat
    IPB000403 Phosphatidylinositol 3- and 4-kinase
    IPB003151 PIK-related kinase


    UniProtKB/Swiss-Prot: SMG1_HUMAN, Q96Q15
    Similarity: Belongs to the PI3/PI4-kinase family
    Similarity: Contains 1 FAT domain
    Similarity: Contains 1 FATC domain
    Similarity: Contains 1 HEAT repeat
    Similarity: Contains 1 PI3K/PI4K domain


    Find genes that share domains with SMG1           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SMG1_HUMAN, Q96Q15
    Function: Serine/threonine protein kinase involved in both mRNA surveillance and genotoxic stress response
    pathways. Recognizes the substrate consensus sequence [ST]-Q. Plays a central role in nonsense-mediated decay
    (NMD) of mRNAs containing premature stop codons by phosphorylating UPF1/RENT1. Recruited by release factors to
    stalled ribosomes together with SMG8 and SMG9 (forming the SMG1C protein kinase complex), and UPF1 to form the
    transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon
    junction complex (EJC) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is
    believed to activate NMD. Also acts as a genotoxic stress-activated protein kinase that displays some functional
    overlap with ATM. Can phosphorylate p53/TP53 and is required for optimal p53/TP53 activation after cellular
    exposure to genotoxic stress. Its depletion leads to spontaneous DNA damage and increased sensitivity to ionizing
    radiation (IR). May activate PRKCI but not PRKCZ
    Catalytic activity: ATP + a protein = ADP + a phosphoprotein
    Enzyme regulation: Inhibited by caffeine, LY294002 and wortmannin

         Enzyme Numbers (IUBMB): EC 2.7.11.11 2 EC 2.7.112

         Gene Ontology (GO): Selected molecular function terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004672protein kinase activity TAS14636577
    GO:0004674protein serine/threonine kinase activity NAS11331269
    GO:0005488binding ----
    GO:0005515protein binding IPI11544179
    GO:0005524ATP binding IEA--
         
    Find genes that share ontologies with SMG1           About GenesLikeMe


    Phenotypes:
         9 GenomeRNAi human phenotypes for SMG1:
     Decreased focal adhesion (FA)   Decreased substrate adherent c  Decreased viability  Increased Salmonella enterica  
     Increased Salmonella enterica   Increased Salmonella enterica   Increased Salmonella-containin  Increased colony dispersion (i 
     Increased gamma-H2AX phosphory 

         15 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Smg1):
     cardiovascular system  cellular  craniofacial  embryogenesis  growth/size/body 
     hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system  mortality/aging 
     nervous system  renal/urinary system  skeleton  tumorigenesis  vision/eye 

    Find genes that share phenotypes with SMG1           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMG1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SMG1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMG1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMG1

    miRNA
    Products:
        
    miRTarBase miRNAs that target SMG1:
    hsa-mir-335-5p (MIRT017428), hsa-mir-92b-3p (MIRT040595), hsa-mir-877-5p (MIRT037357), hsa-mir-106a-5p (MIRT048317), hsa-mir-181a-5p (MIRT047307), hsa-mir-100-5p (MIRT048500), hsa-mir-615-3p (MIRT039989), hsa-mir-17-3p (MIRT050767), hsa-mir-361-5p (MIRT044095), hsa-let-7b-5p (MIRT052316)

    Block miRNA regulation of human, mouse, rat SMG1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMG1 (see all 118):
    hsa-miR-124* hsa-miR-4254 hsa-miR-188-5p hsa-miR-4272 hsa-miR-485-3p hsa-miR-128 hsa-miR-3605-3p hsa-miR-4267
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SMG1

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): SMG1 (NM_003720)
    Browse Sino Biological Human cDNA Clones
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    Cell Line
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMG1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SMG1_HUMAN, Q96Q15: Nucleus. Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol4
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA14636577
    GO:0005737cytoplasm IDA14636577
    GO:0005829cytosol TAS--

    Find genes that share ontologies with SMG1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for SMG1 About    
    See pathways by source

    SuperPathContained pathways About
    1Influenza Viral RNA Transcription and Replication
    Nonsense-Mediated Decay0.89
    Nonsense Mediated Decay Enhanced by the Exon Junction Complex0.89
    2Cell Cycle / Checkpoint Control
    Cell Cycle / Checkpoint Control0.32
    DNA Damage0.32
    3Gene Expression
    Gene Expression0.40
    4mRNA surveillance pathway
    mRNA surveillance pathway


    Find genes that share SuperPaths with SMG1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Cell Signaling Technology (CST) Pathways for SMG1
        Cell Cycle / Checkpoint Control
    DNA Damage

    1 Reactome Pathway for SMG1
        Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)


    1 Kegg Pathway  (Kegg details for SMG1):
        mRNA surveillance pathway

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMG1
    Interactions:

        GeneGlobe Interaction Network for SMG1

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

    Selected Interacting proteins for SMG1 (Q96Q151, 2, 3 ENSP000004025154) via UniProtKB, MINT, STRING, and/or I2D (see all 131)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UPF2Q9HAU51, 2, 3, ENSP000003487084EBI-1049832,EBI-372073 MINT-6539908 I2D: score=3 STRING: ENSP00000348708
    UPF1Q929002, 3, ENSP000002628034MINT-6539908 I2D: score=2 STRING: ENSP00000262803
    UPF3AQ9H1J12, 3, ENSP000003644484MINT-6539908 I2D: score=3 STRING: ENSP00000364448
    TELO2Q9Y4R83, ENSP000002623194I2D: score=3 STRING: ENSP00000262319
    SMG5Q9UPR33, ENSP000003552614I2D: score=2 STRING: ENSP00000355261
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS16488880
    GO:0006281DNA repair IEA--
    GO:0006406mRNA export from nucleus TAS16488880
    GO:0006950response to stress IDA15175154
    GO:0010467gene expression TAS--

    Find genes that share ontologies with SMG1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SMG1

    1 HMDB Compound for SMG1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Manganesemanganese 7439-96-5--

    Selected Novoseek inferred chemical compound relationships for SMG1 gene (see all 19)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    2-chloro-1,4-dimethoxybenzene 95.6 9 9851835 (2), 9845326 (2)
    veratryl alcohol 95.3 50 8203900 (4), 1959597 (3), 7574669 (3), 8639588 (2) (see all 14)
    veratraldehyde 92.8 7 8639588 (1), 7742304 (1), 10749690 (1), 14672691 (1) (see all 6)
    lignin 90.7 46 1397627 (3), 1959597 (1), 8639588 (1), 9136871 (1) (see all 36)
    2-chloro-1,4-benzoquinone 87.9 1 9845326 (1)
    anisyl alcohol 82 2 7864643 (1)
    manganese 54.4 5 19091553 (1), 12802530 (1), 15006517 (1), 12431010 (1)
    phosphatidylinositol 54.1 11 11544179 (2), 16483312 (2), 12356760 (1), 17229728 (1) (see all 9)
    h2o2 51.1 7 7742304 (2), 1959597 (1), 2176851 (1), 8203900 (1)
    tween 80 38.9 4 15006517 (1), 14592442 (1)



    Find genes that share compounds with SMG1           About GenesLikeMe



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SMG1 gene: 
    NM_015092.4  

    Unigene Cluster for SMG1:

    Smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)
    Hs.460179  [show with all ESTs]
    Unigene Representative Sequence: NM_015092
    17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000446231(uc002dfm.3) ENST00000565324(uc021ted.1) ENST00000561940
    ENST00000563448 ENST00000562668 ENST00000569764 ENST00000563235 ENST00000566328
    ENST00000568038 ENST00000561947 ENST00000565224 ENST00000568239 ENST00000532700
    ENST00000569122 ENST00000563836 ENST00000567737 ENST00000389467(uc010bwa.3 uc010bwb.3)

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SMG1 (see all 118):
    hsa-miR-124* hsa-miR-4254 hsa-miR-188-5p hsa-miR-4272 hsa-miR-485-3p hsa-miR-128 hsa-miR-3605-3p hsa-miR-4267
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    Inhib. RNA
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    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SMG1 (NM_003720)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SMG1
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SMG1
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SMG1
      QuantiTect SYBR Green Assays in human, mouse, rat SMG1
      QuantiFast Probe-based Assays in human, mouse, rat SMG1

    Additional mRNA sequence: 

    AB007881.2 AB061371.1 AF186377.1 AF395444.1 AK025794.1 AK057563.1 AK074359.1 AK123332.1 
    AL833298.1 AY014957.1 BC037335.1 BC047629.1 U32581.2 

    Selected DOTS entries (see all 34):

    DT.95169970  DT.40247195  DT.92004155  DT.411389  DT.95160947  DT.92338692  DT.120708827  DT.91684047 
    DT.91877896  DT.120708798  DT.120708824  DT.91650853  DT.91895539  DT.100731230  DT.120708737  DT.120708751 
    DT.120708764  DT.120708774  DT.91653589  DT.91883865  DT.100642736  DT.100656089  DT.100671063  DT.120679583 

    Selected AceView cDNA sequences (see all 151):

    AI215730 AI913153 BQ574742 AA465226 BU742970 CA414897 AA883196 AB007881 
    BQ006195 AW272220 AI720390 BE046015 AI891119 CB115852 AW769065 CB137915 
    CB120824 AA770364 BM750142 AA258676 AW204861 AW467219 BU633006 AA907216 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    SMG1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAAAGATTG
    SMG1 Expression
    About this image


    SMG1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Testis (Reproductive System)
             Testis Somatic Cells Primitive Gonad
     
     Gonad (Reproductive System)
             Testis Somatic Cells Primitive Gonad
    SMG1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMG1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.460179

    UniProtKB/Swiss-Prot: SMG1_HUMAN, Q96Q15
    Tissue specificity: Widely expressed, with highest level in heart and skeletal muscle. Expressed in placenta,
    brain, lung and spleen, but not in liver

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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)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SMG1 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smg11 , 5 SMG1 homolog, phosphatidylinositol 3-kinase-related more1, 5 90.55(n)1
    97.76(a)1
      7 (63.44 cM)5
    2337891  NM_001031814.11  NP_001026984.11 
     1181313085 
    chicken
    (Gallus gallus)
    Aves SMG11 smg-1 homolog, phosphatidylinositol 3-kinase-related more 82.94(n)
    93.5(a)
      416605  XM_414907.4  XP_414907.3 
    lizard
    (Anolis carolinensis)
    Reptilia SMG16
    SMG1 phosphatidylinositol 3-kinase-related kinase
    90(a)
    1 ↔ 1
    GL343769.1(71314-177758)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.235542 Xenopus laevis, Similar to PI-3-kinase-related kinase more 78.11(n)    BC043640.1 
    zebrafish
    (Danio rerio)
    Actinopterygii smg11 PI-3-kinase-related kinase SMG-1 68.25(n)
    74.16(a)
      569810  NM_001080044.2  NP_001073513.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta nonC6
    no-on-and-no-off transient C
    27(a)
    1 → many
    X(6718671-6731573)
    worm
    (Caenorhabditis elegans)
    Secernentea smg-13 kinase 30(a)   I(6909615-6921617)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes TOR26
    PIK-related protein kinase and rapamycin target; s...
    16(a)
    1 → many
    XI(55935-63359) YKL203C


    ENSEMBL Gene Tree for SMG1 (if available)
    TreeFam Gene Tree for SMG1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SMG1 gene
    ENSG000002617402  MTOR2  
    5 SIMAP similar genes for SMG1 using alignment to 10 protein entries:     SMG1_HUMAN (see all proteins):
    DKFZp547E087    61E3.4    BOLA2    MTOR    ATR

    Find genes that share paralogs with SMG1           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for SMG1 (see all 14)
    PGOHUM00000262278 PGOHUM00000262279 PGOHUM00000262280 PGOHUM00000262281 PGOHUM00000248786


    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SMG1 (see all 2518)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0416504
    A breast pleomorphic lobular carcinoma sample4--see VAR_0416502 S C mis40--------
    VAR_0416574
    A breast infiltrating ductal carcinoma sample4--see VAR_0416572 K Q mis40--------
    VAR_0416564
    A breast infiltrating ductal carcinoma sample4--see VAR_0416562 I T mis40--------
    rs669179081,2
    C,F--18818641(+) TGCACCTAT/-  
            
    CTGTC
    1 -- ds50012Minor allele frequency- -:0.50NA CSA 4
    rs720704001,2
    C--18818643(+) CACCT-/ATCT  
            
    GTCAA
    1 -- ds50010--------
    rs26506221,2
    C,F,H--18818669(-) AACAAA/GATTCC 1 -- ds50019Minor allele frequency- G:0.02NS EA NA WA 1202
    rs1845507051,2
    --18819473(+) TGTCAA/GAAAAA 1 -- ut310--------
    rs85601,2
    C,F,A,H--18819483(-) TAGTTT/CTTTCT 1 -- ut31 trp38Minor allele frequency- C:0.27MN NS WA NA EA 668
    rs1876744701,2
    --18819584(+) TTGTAC/TGACAC 1 -- ut310--------
    rs1503006581,2
    --18819617(+) GCTTTC/TTCTAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SMG1 (18816175 - 18937776 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SMG1 (see all 23):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv436205CNV Deletion17901297
    esv2169089CNV Deletion18987734
    esv2632615CNV Deletion19546169
    esv2666793CNV Deletion23128226
    dgv57e180CNV Deletion20482838
    esv2714043CNV Deletion23290073
    nsv1753CNV Insertion18451855
    esv995185CNV Insertion20482838
    nsv833161CNV Loss17160897
    nsv512427CNV Loss21212237

    Human Gene Mutation Database (HGMD): SMG1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMG1
    DNA2.0 Custom Variant and Variant Library Synthesis for SMG1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607032    OMIM disorders: --

    1 disease for SMG1:    
    About MalaCards
    ullrich congenital muscular dystrophy

    1 disease from the University of Copenhagen DISEASES database for SMG1:
    Ullrich congenital muscular dystrophy

    Find genes that share disorders with SMG1           About GenesLikeMe

    1 Novoseek inferred disease relationship for SMG1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ataxia telangiectasia 35.6 1 16483312 (1)


    Export disorders for SMG1 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 SMG1 gene, integrated from 10 sources (see all 115):
    (articles sorted by number of sources associating them with SMG1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. (PubMed id 11331269)1, 2, 3, 9 Denning G.... Fields A.P. (J. Biol. Chem. 2001)
    2. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 9455477)1, 2, 3 Ishikawa K.... Ohara O. (DNA Res. 1997)
    3. Distant N- and C-terminal domains are required for intrinsic kinase activity of SMG-1, a critical component of nonsense-mediated mRNA decay. (PubMed id 17229728)1, 3, 9 Morita T....Ohno S. (J. Biol. Chem. 2007)
    4. SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. (PubMed id 19417104)1, 2, 9 Yamashita A.... Ohno S. (Genes Dev. 2009)
    5. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. (PubMed id 11544179)1, 2, 9 Yamashita A.... Ohno S. (Genes Dev. 2001)
    6. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PubMed id 12554878)1, 2, 9 Chiu S.-Y.... Maquat L.E. (RNA 2003)
    7. AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay. (PubMed id 20371770)1, 2, 9 Izumi N.... Ohno S. (Sci. Signal. 2010)
    8. The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large- scale conformational changes controlled by SMG-8. (PubMed id 21245168)1, 2 Arias-Palomo E.... Llorca O. (Genes Dev. 2011)
    9. Tti1 and Tel2 are critical factors in mammalian target of rapamycin complex assembly. (PubMed id 20427287)1, 2 Kaizuka T.... Mizushima N. (J. Biol. Chem. 2010)
    10. Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. (PubMed id 16452507)1, 2 Kashima I.... Ohno S. (Genes Dev. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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)
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    Entrez Gene: 23049 HGNC: 30045 AceView: SMG1 Ensembl:ENSG00000157106 euGenes: HUgn23049
    ECgene: SMG1 Kegg: 23049 H-InvDB: SMG1

    (According to HUGE)
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    HUGE: KIAA0421

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SMG1 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 SMG1 gene:
    Search GeneIP for patents involving SMG1

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



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