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

Gene ID: 23049, updated on 30-Aug-2020

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
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

Genomic context

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See SMG1 in Genome Data Viewer
Location:
16p12.3
Exon count:
65
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (18804858..18926428, 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

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. 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
  2. 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
  3. 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
  4. 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
  5. Genetic screen identifies suppressor of morphogenesis in genitalia-1 (SMG-1) as a modulator of sorafenib resistance in hepatocellular carcinoma cell lines. Nam SW, et al. Int J Oncol, 2014 Oct. PMID 25017961

See all (70) 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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Knock down of the expression of SMG-1 inhibited tumor cell proliferation and induced the chemosensitivity of pancreatic cancer cells in vitro.
    Title: Overexpression of serine/threonine-protein kinase-1 in pancreatic cancer tissue: Serine/threonine-protein kinase-1 knockdown increases the chemosensitivity of pancreatic cancer cells.
  8. SMG1 was hypermethylated in 66% of AML samples compared with none in controls. mTOR expression level was negatively correlated to SMG1 expression in AML patients which indicated that SMG1 and mTOR maybe act antagonistically to regulate AML cell growth.
    Title: SMG1 acts as a novel potential tumor suppressor with epigenetic inactivation in acute myeloid leukemia.
  9. A genome-wide RNA interference screen Hepatocellular carcinoma cell lines revealed the role of suppressor of SMG-1 as determinant of sorafenib resistance.
    Title: Genetic screen identifies suppressor of morphogenesis in genitalia-1 (SMG-1) as a modulator of sorafenib resistance in hepatocellular carcinoma cell lines.
  10. SMG1 regulates NMD by recruiting UPF1 and UPF2 to distinct nearby positions, and can form a complex with UPF2 in vivo in an UPF1-independent manner.
    Title: Structures of SMG1-UPFs complexes: SMG1 contributes to regulate UPF2-dependent activation of UPF1 in NMD.
Submit: New GeneRIF Correction See all GeneRIFs (34)

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
ATP binding IEA
Inferred from Electronic Annotation
more info
  
RNA binding HDA 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 IBA
Inferred from Biological aspect of Ancestor
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 
Process Evidence Code Pubs
DNA repair IEA
Inferred from Electronic Annotation
more info
  
TORC1 signaling IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 PubMed 
negative regulation of autophagy IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
negative regulation of macroautophagy IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
Inferred from Direct Assay
more info
 PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay NAS
Non-traceable Author Statement
more info
 PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
 PubMed 
peptidyl-serine phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
peptidyl-serine phosphorylation TAS
Traceable Author Statement
more info
 PubMed 
phosphatidylinositol phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
protein autophosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
regulation of response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
regulation of telomere maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
TORC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
TORC2 complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
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_024305966.1
XP_024305967.1

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
    Related
    ENSP00000402515.2, ENST00000446231.6
    Conserved Domains (3) 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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    18804858..18926428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255183.4 → 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

  2. XM_005255184.4 → XP_005255241.1  serine/threonine-protein kinase SMG1 isoform X4

    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_011545769.3 → 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

  4. XM_024450198.1 → XP_024305966.1  serine/threonine-protein kinase SMG1 isoform X5

    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

  5. XM_005255182.3 → 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_024450199.1 → XP_024305967.1  serine/threonine-protein kinase SMG1 isoform X5

    Related
    ENSP00000456259.1, ENST00000565324.5
    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

  7. XM_017023066.2 → 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

  8. XM_011545770.1 → XP_011544072.1  serine/threonine-protein kinase SMG1 isoform X6

    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

  9. XM_017023067.1 → XP_016878556.1  serine/threonine-protein kinase SMG1 isoform X6

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

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