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    SMG1 SMG1, nonsense mediated mRNA decay associated PI3K related kinase [ Homo sapiens (human) ]

    Gene ID: 23049, updated on 18-Mar-2017
    Official Symbol
    SMG1provided by HGNC
    Official Full Name
    SMG1, nonsense mediated mRNA decay associated PI3K related kinaseprovided by HGNC
    Primary source
    HGNC:HGNC:30045
    See related
    Ensembl:ENSG00000157106 MIM:607032; Vega:OTTHUMG00000166900
    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
    ATX; LIP; 61E3.4
    Summary
    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]
    Orthologs
    Location:
    16p12.3
    Exon count:
    64
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 16 NC_000016.10 (18804853..18926417, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (18816175..18937748, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S15a Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 1 Neighboring gene putative uncharacterized protein encoded by LINC00269 Neighboring gene uncharacterized LOC107984844 Neighboring gene transmembrane channel like 7 Neighboring gene RNA, U6 small nuclear 1340, pseudogene Neighboring gene uncharacterized LOC102723385 Neighboring gene coenzyme Q7, hydroxylase

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • 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...
    • Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
      Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystemDuring normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of trans...
    • Nonsense-Mediated Decay (NMD), organism-specific biosystem (from REACTOME)
      Nonsense-Mediated Decay (NMD), organism-specific biosystemThe Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. ...
    • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
      mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    • mRNA surveillance pathway, conserved biosystem (from KEGG)
      mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA0421

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    protein serine/threonine kinase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein serine/threonine kinase activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    serine/threonine-protein kinase SMG1
    Names
    PI-3-kinase-related kinase SMG-1
    SMG1 phosphatidylinositol 3-kinase-related kinase
    lambda-interacting protein
    lambda/iota protein kinase C-interacting protein
    smg-1 homolog, phosphatidylinositol 3-kinase-related kinase
    NP_055907.3

    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_015092.4NP_055907.3  serine/threonine-protein kinase SMG1

      See identical proteins and their annotated locations for NP_055907.3

      Status: REVIEWED

      Source sequence(s)
      AB061371, AK025794, AL833298, AW088221, AW503964, AY014957, BC037335, BE079340, DA433527, DA854035
      Consensus CDS
      CCDS45430.1
      UniProtKB/Swiss-Prot
      Q96Q15
      Related
      ENSP00000402515, OTTHUMP00000234388, ENST00000446231, OTTHUMT00000391817
      Conserved Domains (3) summary
      cd05170
      Location:21212426
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36313660
      FATC; FATC domain
      pfam15785
      Location:6311242
      SMG1; Serine/threonine-protein kinase smg-1

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 Primary Assembly

      Range
      18804853..18926417 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255184.3XP_005255241.1  serine/threonine-protein kinase SMG1 isoform X4

      Related
      ENSP00000456259, OTTHUMP00000256093, ENST00000565324, OTTHUMT00000435790
      Conserved Domains (3) summary
      cd05170
      Location:20692402
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36073636
      FATC; FATC domain
      pfam15785
      Location:5791190
      SMG1; Serine/threonine-protein kinase smg-1
    2. XM_011545769.2XP_011544071.1  serine/threonine-protein kinase SMG1 isoform X2

      Conserved Domains (3) summary
      cd05170
      Location:21212454
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36583687
      FATC; FATC domain
      pfam15785
      Location:6311242
      SMG1; Serine/threonine-protein kinase smg-1
    3. XM_005255182.3XP_005255239.1  serine/threonine-protein kinase SMG1 isoform X1

      Conserved Domains (3) summary
      cd05170
      Location:21212454
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36593688
      FATC; FATC domain
      pfam15785
      Location:6311242
      SMG1; Serine/threonine-protein kinase smg-1
    4. XM_005255183.3XP_005255240.1  serine/threonine-protein kinase SMG1 isoform X3

      Conserved Domains (3) summary
      cd05170
      Location:20952428
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36333662
      FATC; FATC domain
      pfam15785
      Location:6051216
      SMG1; Serine/threonine-protein kinase smg-1
    5. XM_017023066.1XP_016878555.1  serine/threonine-protein kinase SMG1 isoform X3

      Conserved Domains (3) summary
      cd05170
      Location:20952428
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:36333662
      FATC; FATC domain
      pfam15785
      Location:6051216
      SMG1; Serine/threonine-protein kinase smg-1
    6. XM_011545770.1XP_011544072.1  serine/threonine-protein kinase SMG1 isoform X5

      Conserved Domains (3) summary
      cd05170
      Location:14911824
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:30293058
      FATC; FATC domain
      pfam15785
      Location:1612
      SMG1; Serine/threonine-protein kinase smg-1
    7. XM_017023067.1XP_016878556.1  serine/threonine-protein kinase SMG1 isoform X5

      Conserved Domains (3) summary
      cd05170
      Location:14911824
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:30293058
      FATC; FATC domain
      pfam15785
      Location:1612
      SMG1; Serine/threonine-protein kinase smg-1

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      18903656..19025005 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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