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Aliases for SMG1 Gene

Aliases for SMG1 Gene

  • SMG1 Phosphatidylinositol 3-Kinase-Related Kinase 2 3
  • LIP 3 4 6
  • Lambda/Iota Protein Kinase C-Interacting Protein 3 4
  • Lambda-Interacting Protein 3 4
  • EC 2.7.11.1 4 64
  • KIAA0421 4 6
  • 61E3.4 3 4
  • ATX 3 4
  • Smg-1 Homolog, Phosphatidylinositol 3-Kinase-Related Kinase (C. Elegans) 2
  • Smg-1 Homolog, Phosphatidylinositol 3-Kinase-Related Kinase 3
  • Phosphatidylinositol 3-Kinase-Related Kinase 2
  • Serine/Threonine-Protein Kinase SMG1 3
  • PI-3-Kinase-Related Kinase SMG-1 3
  • EC 2.7.11 64
  • HSMG-1 4
  • SMG-1 4

External Ids for SMG1 Gene

Summaries for SMG1 Gene

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. Among its related pathways are Cell Cycle / Checkpoint Control and Gene Expression. 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 for SMG1 Gene

  • 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMG1 Gene

Genomics for SMG1 Gene

Genomic Location for SMG1 Gene

Start:
18,804,853 bp from pter
End:
18,926,454 bp from pter
Size:
121,602 bases
Orientation:
Minus strand

Genomic View for SMG1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMG1 Gene

Proteins for SMG1 Gene

  • Protein details for SMG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96Q15-SMG1_HUMAN
    Recommended name:
    Serine/threonine-protein kinase SMG1
    Protein Accession:
    Q96Q15
    Secondary Accessions:
    • O43305
    • Q13284
    • Q8NFX2
    • Q96QV0
    • Q96RW3

    Protein attributes for SMG1 Gene

    Size:
    3661 amino acids
    Molecular mass:
    410501 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • 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
    SequenceCaution:
    • Sequence=AAA86535.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SMG1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMG1 Gene

Proteomics data for SMG1 Gene at MOPED

Selected DME Specific Peptides for SMG1 Gene

Post-translational modifications for SMG1 Gene

Domains for SMG1 Gene

UniProtKB/Swiss-Prot:

SMG1_HUMAN
Domain:
  • Contains 1 FAT domain.:
    • Q96Q15
  • Contains 1 FATC domain.:
    • Q96Q15
  • Contains 1 PI3K/PI4K domain.:
    • Q96Q15
Family:
  • Belongs to the PI3/PI4-kinase family.:
    • Q96Q15
Similarity:
  • Contains 1 HEAT repeat.:
    • Q96Q15
genes like me logo Genes that share domains with SMG1: view

Function for SMG1 Gene

Molecular function for SMG1 Gene

UniProtKB/Swiss-Prot CatalyticActivity: ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot EnzymeRegulation: Inhibited by caffeine, LY294002 and wortmannin.
UniProtKB/Swiss-Prot 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.

Enzyme Numbers (IUBMB) for SMG1 Gene

Gene Ontology (GO) - Molecular Function for SMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity TAS 14636577
GO:0004674 protein serine/threonine kinase activity NAS 11331269
GO:0005488 binding --
GO:0005515 protein binding IPI 11544179
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SMG1: view
genes like me logo Genes that share phenotypes with SMG1: view

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for SMG1 Gene

Localization for SMG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMG1 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMG1 Gene COMPARTMENTS Subcellular localization image for SMG1 gene
Compartment Confidence
nucleus 5
cytosol 4
mitochondrion 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 14636577
GO:0005737 cytoplasm IDA 14636577
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SMG1: view

Pathways for SMG1 Gene

genes like me logo Genes that share pathways with SMG1: view

Pathways by source for SMG1 Gene

1 KEGG pathway for SMG1 Gene

Gene Ontology (GO) - Biological Process for SMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS 16488880
GO:0000724 double-strand break repair via homologous recombination IBA --
GO:0006281 DNA repair --
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0006950 response to stress IDA 15175154
genes like me logo Genes that share ontologies with SMG1: view

Compounds for SMG1 Gene

(1) HMDB Compounds for SMG1 Gene

Compound Synonyms Cas Number PubMed IDs
Manganese
  • manganese
7439-96-5

(19) Novoseek inferred chemical compound relationships for SMG1 Gene

Compound -log(P) Hits PubMed IDs
2-chloro-1,4-dimethoxybenzene 95.6 4
veratryl alcohol 95.3 26
veratraldehyde 92.8 6
lignin 90.7 38
2-chloro-1,4-benzoquinone 87.9 1
genes like me logo Genes that share compounds with SMG1: view

Transcripts for SMG1 Gene

Unigene Clusters for SMG1 Gene

Smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMG1 Gene

No ASD Table

Relevant External Links for SMG1 Gene

GeneLoc Exon Structure for
SMG1
ECgene alternative splicing isoforms for
SMG1

Expression for SMG1 Gene

mRNA expression in normal human tissues for SMG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMG1 Gene

This gene is overexpressed in Muscle - Skeletal (4.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMG1 Gene

SOURCE GeneReport for Unigene cluster for SMG1 Gene Hs.460179

mRNA Expression by UniProt/SwissProt for SMG1 Gene

Q96Q15-SMG1_HUMAN
Tissue specificity: Widely expressed, with highest level in heart and skeletal muscle. Expressed in placenta, brain, lung and spleen, but not in liver.
genes like me logo Genes that share expressions with SMG1: view

Orthologs for SMG1 Gene

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

Orthologs for SMG1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMG1 36
  • 99.62 (n)
  • 99.86 (a)
SMG1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMG1 36
  • 92.98 (n)
  • 98.96 (a)
SMG1 37
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMG1 36
  • 93.37 (n)
  • 98.79 (a)
SMG1 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smg1 36
  • 90.55 (n)
  • 97.76 (a)
Smg1 16
Smg1 37
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMG1 37
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMG1 37
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smg1 36
  • 89.38 (n)
  • 96.59 (a)
chicken
(Gallus gallus)
Aves SMG1 36
  • 82.94 (n)
  • 93.5 (a)
SMG1 37
  • 93 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMG1 37
  • 90 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.23554 36
tropical clawed frog
(Silurana tropicalis)
Amphibia smg1 36
  • 77.25 (n)
  • 86.01 (a)
zebrafish
(Danio rerio)
Actinopterygii smg1 36
  • 68.25 (n)
  • 74.16 (a)
smg1 37
  • 74 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta nonC 37
  • 27 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-1 37
  • 24 (a)
OneToMany
smg-1 38
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TOR2 37
  • 16 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6873 36
Species with no ortholog for SMG1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMG1 Gene

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

Paralogs for SMG1 Gene

Paralogs for SMG1 Gene

genes like me logo Genes that share paralogs with SMG1: view

Variants for SMG1 Gene

Sequence variations from dbSNP and Humsavar for SMG1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs8560 -- 18,805,278(-) TAGTT(C/T)TTTCT utr-variant-3-prime
rs9803 -- 18,805,296(+) GTTTT(C/G)AAAGA utr-variant-3-prime
rs735173 -- 18,828,466(+) GTTAA(G/T)TACAA intron-variant
rs904821 -- 18,828,350(-) AGAAG(A/T)CTTTC intron-variant
rs1809907 -- 18,828,913(-) TCAAG(C/T)GATTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMG1 Gene

Variant ID Type Subtype PubMed ID
esv587 CNV CNV 17122850
dgv822e1 CNV Complex 17122850
dgv823e1 CNV Complex 17122850
nsv428320 CNV Loss 18775914
esv34419 CNV Gain 17911159
dgv825e1 CNV Complex 17122850
nsv469598 CNV Gain 16826518
nsv833161 CNV Loss 17160897
nsv1752 CNV Loss 18451855
nsv512427 CNV Loss 21212237
nsv436205 CNV Deletion 17901297
esv2169089 CNV Deletion 18987734
dgv57e180 CNV Deletion 20482838
esv2632615 CNV Deletion 19546169
esv2714043 CNV Deletion 23290073
nsv1753 CNV Insertion 18451855
esv995185 CNV Insertion 20482838
esv22839 CNV Gain 19812545
nsv905556 CNV Gain 21882294
nsv9385 CNV Loss 18304495
nsv905557 CNV Gain 21882294
esv2666793 CNV Deletion 23128226
nsv9386 CNV Loss 18304495

Relevant External Links for SMG1 Gene

HapMap Linkage Disequilibrium report
SMG1

Disorders for SMG1 Gene

(1) University of Copenhagen DISEASES for SMG1 Gene

(1) Novoseek inferred disease relationships for SMG1 Gene

Disease -log(P) Hits PubMed IDs
ataxia telangiectasia 35.6 1
genes like me logo Genes that share disorders with SMG1: view

No data available for UniProtKB/Swiss-Prot for SMG1 Gene

Publications for SMG1 Gene

  1. Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. (PMID: 11331269) Denning G. … Fields A.P. (J. Biol. Chem. 2001) 2 3 4 23
  2. 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. (PMID: 11544179) Yamashita A. … Ohno S. (Genes Dev. 2001) 3 4 23
  3. Distant N- and C-terminal domains are required for intrinsic kinase activity of SMG-1, a critical component of nonsense-mediated mRNA decay. (PMID: 17229728) Morita T. … Ohno S. (J. Biol. Chem. 2007) 2 3 23
  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. (PMID: 19417104) Yamashita A. … Ohno S. (Genes Dev. 2009) 3 4 23
  5. AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay. (PMID: 20371770) Izumi N. … Ohno S. (Sci. Signal. 2010) 3 4 23

Products for SMG1 Gene

Sources for SMG1 Gene

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