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

Gene ID: 23049, updated on 5-Aug-2022

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
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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
110 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (18804860..18926408, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (18741287..18857007, complement)
105.20220307 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 ribosomal protein S15a Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 1 Neighboring gene small nucleolar RNA U13 Neighboring gene putative uncharacterized protein encoded by LINC00269 Neighboring gene SMG1 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 10247 Neighboring gene transmembrane channel like 7 Neighboring gene RNA, U6 small nuclear 1340, pseudogene

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. Large-scale genomic sequencing reveals adaptive opportunity of targeting mutated-PI3Kα in early and advanced HER2-positive breast cancer. Guo LW, et al. Clin Transl Med, 2021 Nov. PMID 34842356, 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 (93) citations in PubMed

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. SMG1 and CDK12 Link DeltaNp63alpha Phosphorylation to RNA Surveillance in Keratinocytes.
    Title: SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes.
  3. 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.
  4. Cryo-EM structure of SMG1-SMG8-SMG9 complex.
    Title: Cryo-EM structure of SMG1-SMG8-SMG9 complex.
  5. 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.
  6. 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.
  7. 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<sub>6</sub> binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
  8. 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.
  9. 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.
  10. ionizing radiation (IR) inhibits the activity of SMG1, a phosphoinositide-3-kinase-like kinase family member, reducing the binding of SMG1 to a specific region near exon 9 of p53 precursor mRNA and promoting the binding of ribosomal protein L26 (RPL26) to p53 pre-mRNA
    Title: Identification of a DNA Damage-Induced Alternative Splicing Pathway That Regulates p53 and Cellular Senescence Markers.
Submit: New GeneRIF Correction See all GeneRIFs (38)

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)

Genotypes

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 ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
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 C activity EXP
Inferred from Experiment
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
 PubMed 
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 telomeric DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in mRNA export from nucleus TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of macroautophagy IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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 protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in regulation of response to DNA damage stimulus 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
part_of TORC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
part_of TORC2 complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
 PubMed 
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

NCBI Reference Sequences (RefSeq)

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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
    Q96Q15, Q96RW3
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    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

    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

    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

    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

    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

    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

    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

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

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