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

    Gene ID: 23049, updated on 27-Nov-2024

    Summary

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    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; AllianceGenome:HGNC:30045
    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]
    Expression
    Ubiquitous expression in skin (RPKM 20.7), bone marrow (RPKM 12.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMG1 in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    66
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (18804860..18926408, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (18741287..18857007, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (18816182..18937730, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:18800609-18801326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10521 Neighboring gene ribosomal protein S15a Neighboring gene ARL6 interacting reticulophagy regulator 1 Neighboring gene small nucleolar RNA U13 Neighboring gene putative uncharacterized protein encoded by LINC00269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:18922767-18923268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10522 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7237 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:18937597-18938209 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:18938210-18938823 Neighboring gene SMG1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:18983611-18984111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7239 Neighboring gene Sharpr-MPRA regulatory region 10247 Neighboring gene transmembrane channel like 7 Neighboring gene RNA, U6 small nuclear 1340, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19041109-19041653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7240 Neighboring gene COQ7 divergent transcript Neighboring gene coenzyme Q7, hydroxylase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Downregulation of SMG-1 in HPV-positive head and neck squamous cell carcinoma due to promoter hypermethylation correlates with improved survival. Gubanova E, et al. Clin Cancer Res, 2012 Mar 1. PMID 22247495, Free PMC Article
    2. A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene. Wong C, et al. PLoS Genet, 2019 Aug. PMID 31469826, Free PMC Article
    3. SMG-1 kinase attenuates mitochondrial ROS production but not cell respiration deficits during hyperoxia. Resseguie EA, et al. Exp Lung Res, 2017 Aug-Sep. PMID 28749708, Free PMC Article
    4. Overexpression of serine/threonine-protein kinase-1 in pancreatic cancer tissue: Serine/threonine-protein kinase-1 knockdown increases the chemosensitivity of pancreatic cancer cells. Wang Q, et al. Mol Med Rep, 2015 Jul. PMID 25760059
    5. SMG1 acts as a novel potential tumor suppressor with epigenetic inactivation in acute myeloid leukemia. Du Y, et al. Int J Mol Sci, 2014 Sep 25. PMID 25257528, Free PMC Article

    See all (108) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMG1, a nonsense-mediated mRNA decay (NMD) regulator, as a candidate therapeutic target in multiple myeloma.
      Title: SMG1, a nonsense-mediated mRNA decay (NMD) regulator, as a candidate therapeutic target in multiple myeloma.
    2. Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kalpha in early and advanced HER2-positive breast cancer.
      Title: Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kα in early and advanced HER2-positive breast cancer.
    3. SMG1 and CDK12 Link DeltaNp63alpha Phosphorylation to RNA Surveillance in Keratinocytes.
      Title: SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes.
    4. Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
      Title: Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
    5. Cryo-EM structure of SMG1-SMG8-SMG9 complex.
      Title: Cryo-EM structure of SMG1-SMG8-SMG9 complex.
    6. MicroRNA-18a promotes cancer progression through SMG1 suppression and mTOR pathway activation in nasopharyngeal carcinoma.
      Title: MicroRNA-18a promotes cancer progression through SMG1 suppression and mTOR pathway activation in nasopharyngeal carcinoma.
    7. SMG1 variants c.4249A>G and c.103G>A are associated with pancreatic cancer in large study
      Title: A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene.
    8. This study reports the 3.45-A resolution cryo-EM structure of human SMG1-SMG8-SMG9, a phosphatidylinositol-3-kinase (PI(3)K)-related protein kinase (PIKK) complex central to messenger RNA surveillance.
      Title: InsP(6) binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
    9. SMG-1 is a target of the oncomiRs, miR-192 and -215, and that its downregulation is associated with tumor size and serosal invasion of gastric cancer (GC). SMG-1 appears to mediate at least some of the oncogenic function of miR-192 and -215 by participating in epithelial-mesenchymal transition, triggered by activation of the Wnt pathway in GC.
      Title: SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling.
    10. Because SMG-1-p53 signaling attenuates production of mitochondrial ROS.
      Title: SMG-1 kinase attenuates mitochondrial ROS production but not cell respiration deficits during hyperoxia.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0421

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3-phosphoinositide-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables AMP-activated protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-dependent protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables Rho-dependent protein serine/threonine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables diacylglycerol-dependent serine/threonine kinase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables eukaryotic translation initiation factor 2alpha kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AS1 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AS121 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AT120 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AXS139 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2BS14 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2BS36 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S10 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S28 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3S57 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T11 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T3 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T45 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3T6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4S1 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein serine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein serine/threonine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein serine/threonine kinase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables ribosomal protein S6 kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables telomeric DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA export from nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in peptidyl-serine phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peptidyl-serine phosphorylation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phosphatidylinositol phosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein autophosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of telomere maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatoid body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    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
    nonsense mediated mRNA decay-associated PI3K-related kinase SMG1
    smg-1 homolog, phosphatidylinositol 3-kinase-related kinase
    NP_055907.3
    XP_005255239.1
    XP_005255240.1
    XP_005255241.1
    XP_011544071.1
    XP_011544072.1
    XP_016878555.1
    XP_016878556.1
    XP_024305967.1
    XP_047289748.1
    XP_047289749.1
    XP_047289750.1
    XP_047289751.1
    XP_047289752.1
    XP_054235809.1
    XP_054235810.1
    XP_054235811.1
    XP_054235812.1
    XP_054235813.1
    XP_054235814.1
    XP_054235815.1
    XP_054235816.1
    XP_054235817.1
    XP_054235818.1
    XP_054235819.1
    XP_054235820.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_015092.5 → NP_055907.3  serine/threonine-protein kinase SMG1

      See identical proteins and their annotated locations for NP_055907.3

      Status: REVIEWED

      Source sequence(s)
      AB061371, AC138811, AK025794, AL833298, AW088221, AW503964, AY014957, BC037335, BE079340, DA433527, DA854035
      Consensus CDS
      CCDS45430.1
      UniProtKB/Swiss-Prot
      O43305, Q13284, Q8NFX2, Q96Q15, Q96QV0, Q96RW3
      UniProtKB/TrEMBL
      J3KRA9
      Related
      ENSP00000402515.3, ENST00000446231.7
      Conserved Domains (4) summary
      cd05170
      Location:2121 → 2426
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3631 → 3660
      FATC; FATC domain
      pfam15785
      Location:631 → 1242
      SMG1; Serine/threonine-protein kinase smg-1
      pfam17229
      Location:32 → 140
      DUF5303; Region of unknown function (DUF5303)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      18804860..18926408 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433796.1 → XP_047289752.1  serine/threonine-protein kinase SMG1 isoform X8

      Related
      ENSP00000456259.1, ENST00000565324.5

    2. XM_005255184.5 → XP_005255241.1  serine/threonine-protein kinase SMG1 isoform X5

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2069 → 2402
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3607 → 3636
      FATC; FATC domain
      pfam15785
      Location:579 → 1190
      SMG1; Serine/threonine-protein kinase smg-1

    3. XM_047433793.1 → XP_047289749.1  serine/threonine-protein kinase SMG1 isoform X4

    4. XM_011545769.4 → XP_011544071.1  serine/threonine-protein kinase SMG1 isoform X2

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2121 → 2454
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3658 → 3687
      FATC; FATC domain
      pfam15785
      Location:631 → 1242
      SMG1; Serine/threonine-protein kinase smg-1

    5. XM_005255182.4 → XP_005255239.1  serine/threonine-protein kinase SMG1 isoform X1

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2121 → 2454
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3659 → 3688
      FATC; FATC domain
      pfam15785
      Location:631 → 1242
      SMG1; Serine/threonine-protein kinase smg-1

    6. XM_005255183.5 → XP_005255240.1  serine/threonine-protein kinase SMG1 isoform X3

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2095 → 2428
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3633 → 3662
      FATC; FATC domain
      pfam15785
      Location:605 → 1216
      SMG1; Serine/threonine-protein kinase smg-1

    7. XM_047433794.1 → XP_047289750.1  serine/threonine-protein kinase SMG1 isoform X6

    8. XM_017023066.3 → XP_016878555.1  serine/threonine-protein kinase SMG1 isoform X3

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2095 → 2428
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3633 → 3662
      FATC; FATC domain
      pfam15785
      Location:605 → 1216
      SMG1; Serine/threonine-protein kinase smg-1

    9. XM_047433795.1 → XP_047289751.1  serine/threonine-protein kinase SMG1 isoform X7

    10. XM_024450199.2 → XP_024305967.1  serine/threonine-protein kinase SMG1 isoform X7

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:2043 → 2376
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3581 → 3610
      FATC; FATC domain
      pfam15785
      Location:553 → 1162
      SMG1; Serine/threonine-protein kinase smg-1

    11. XM_047433792.1 → XP_047289748.1  serine/threonine-protein kinase SMG1 isoform X3

    12. XM_011545770.2 → XP_011544072.1  serine/threonine-protein kinase SMG1 isoform X9

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:1491 → 1824
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3029 → 3058
      FATC; FATC domain
      pfam15785
      Location:1 → 612
      SMG1; Serine/threonine-protein kinase smg-1

    13. XM_017023067.2 → XP_016878556.1  serine/threonine-protein kinase SMG1 isoform X9

      UniProtKB/TrEMBL
      J3KRA9
      Conserved Domains (3) summary
      cd05170
      Location:1491 → 1824
      PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
      pfam02260
      Location:3029 → 3058
      FATC; FATC domain
      pfam15785
      Location:1 → 612
      SMG1; Serine/threonine-protein kinase smg-1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      18741287..18857007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379844.1 → XP_054235819.1  serine/threonine-protein kinase SMG1 isoform X8

    2. XM_054379840.1 → XP_054235815.1  serine/threonine-protein kinase SMG1 isoform X5

    3. XM_054379839.1 → XP_054235814.1  serine/threonine-protein kinase SMG1 isoform X4

    4. XM_054379835.1 → XP_054235810.1  serine/threonine-protein kinase SMG1 isoform X2

    5. XM_054379834.1 → XP_054235809.1  serine/threonine-protein kinase SMG1 isoform X1

    6. XM_054379838.1 → XP_054235813.1  serine/threonine-protein kinase SMG1 isoform X3

    7. XM_054379841.1 → XP_054235816.1  serine/threonine-protein kinase SMG1 isoform X6

    8. XM_054379836.1 → XP_054235811.1  serine/threonine-protein kinase SMG1 isoform X3

    9. XM_054379842.1 → XP_054235817.1  serine/threonine-protein kinase SMG1 isoform X7

    10. XM_054379843.1 → XP_054235818.1  serine/threonine-protein kinase SMG1 isoform X7

    11. XM_054379837.1 → XP_054235812.1  serine/threonine-protein kinase SMG1 isoform X3

    12. XM_054379845.1 → XP_054235820.1  serine/threonine-protein kinase SMG1 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96Q15.3 GenPept UniProtKB/Swiss-Prot:Q96Q15

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