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Aliases for SMG1 Gene

Aliases for SMG1 Gene

  • SMG1, Nonsense Mediated MRNA Decay Associated PI3K Related Kinase 2 3 5
  • SMG1 Phosphatidylinositol 3-Kinase-Related Kinase 2 3
  • Lambda/Iota Protein Kinase C-Interacting Protein 3 4
  • Lambda-Interacting Protein 3 4
  • EC 2.7.11.1 4 58
  • 61E3.4 3 4
  • LIP 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 58
  • KIAA0421 4
  • HSMG-1 4
  • SMG-1 4

External Ids for SMG1 Gene

Previous GeneCards Identifiers for SMG1 Gene

  • GC16M018309
  • GC16M018746
  • GC16M018785
  • GC16M018726
  • GC16M017358

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, Nonsense Mediated MRNA Decay Associated PI3K Related Kinase) is a Protein Coding gene. Among its related pathways are DNA Damage and mRNA surveillance pathway. GO annotations related to this gene include poly(A) RNA binding and protein kinase activity. An important paralog of this gene is MTOR.

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

Additional gene information for SMG1 Gene

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

Genomics for SMG1 Gene

Regulatory Elements for SMG1 Gene

Enhancers for SMG1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H018797 1.8 FANTOM5 ENCODE dbSUPER 11.9 +124.1 124133 9 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 ZC3H11A NFYC ENSG00000260017 ARL6IP1 ENSG00000262974 ENSG00000260242 SMG1 RPS15A ENSG00000205746 COQ7
GH16H018969 1.2 Ensembl ENCODE 12.6 -42.9 -42880 0 FOXA2 MLX ARID4B FEZF1 ZNF2 SLC30A9 GLIS2 ZNF143 DEK MXD4 SMG1 RNU6-1340P COQ7 TMC7 ENSG00000260352
GH16H019409 1.1 Ensembl ENCODE 10.4 -484.4 -484428 1 SIN3A ZNF2 GTF3C2 ZNF121 GLIS2 SCRT2 ATF7 DEK ZEB2 ZNF398 TMC5 SYT17 RPS15A SMG1 ENSG00000259925 KNOP1 ENSG00000260681
GH16H019804 1.1 Ensembl ENCODE 10.3 -880.8 -880785 6 BCOR PKNOX1 NFIB JUN MAX EBF1 BATF ZNF316 RBAK POLR2A KNOP1 THUMPD1 SMG1 ACSM5 LARP7P2 LOC105371115
GH16H018955 0.8 Ensembl ENCODE 12.6 -29.8 -29847 1 DRAP1 SAP130 POLR2A FOXK2 NRF1 DMAP1 KAT8 SMG1 ARL6IP1 ENSG00000260352 TMC7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMG1 on UCSC Golden Path with GeneCards custom track

Promoters for SMG1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000084116 554 3001 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2

Genomic Location for SMG1 Gene

Chromosome:
16
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

Genes around SMG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Selected DME Specific Peptides for SMG1 Gene

Q96Q15:
  • TGEVVHID
  • VLRGCLE
  • LPTKTKPKK
  • DPLVDWT

Post-translational modifications for SMG1 Gene

Domains & Families for SMG1 Gene

Gene Families for SMG1 Gene

Suggested Antigen Peptide Sequences for SMG1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96Q15

UniProtKB/Swiss-Prot:

SMG1_HUMAN :
  • Belongs to the PI3/PI4-kinase family.
Family:
  • Belongs to the PI3/PI4-kinase family.
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:0003723 RNA binding IDA 22681889
GO:0004672 protein kinase activity TAS 14636577
GO:0004674 protein serine/threonine kinase activity IEA,NAS 11331269
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

Animal Model Products

CRISPR Products

miRNA for SMG1 Gene

miRTarBase miRNAs that target SMG1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMG1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMG1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 14636577
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 14636577
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SMG1: view

Pathways & Interactions for SMG1 Gene

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

Pathways by source for SMG1 Gene

1 Cell Signaling Technology pathway for SMG1 Gene
1 KEGG pathway for SMG1 Gene

SIGNOR curated interactions for SMG1 Gene

Activates:

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 IEA,TAS 16488880
GO:0006281 DNA repair IBA --
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0006468 protein phosphorylation IEA --
GO:0006950 response to stress IDA 15175154
genes like me logo Genes that share ontologies with SMG1: view

Drugs & Compounds for SMG1 Gene

(7) Drugs for SMG1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 35

(12) Additional Compounds for SMG1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SMG1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x4.5).

Protein differential expression in normal tissues from HIPED for SMG1 Gene

This gene is overexpressed in Salivary gland (15.4), Breast (10.8), and Cerebrospinal fluid (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMG1 Gene



Protein tissue co-expression partners for SMG1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SMG1 Gene:

SMG1

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.

Evidence on tissue expression from TISSUES for SMG1 Gene

  • Nervous system(4.8)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with SMG1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SMG1 Gene

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 33 34
  • 99.62 (n)
oppossum
(Monodelphis domestica)
Mammalia SMG1 34
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMG1 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMG1 33 34
  • 93.37 (n)
cow
(Bos Taurus)
Mammalia SMG1 33 34
  • 92.98 (n)
mouse
(Mus musculus)
Mammalia Smg1 33 16 34
  • 90.55 (n)
rat
(Rattus norvegicus)
Mammalia Smg1 33
  • 89.38 (n)
chicken
(Gallus gallus)
Aves SMG1 33 34
  • 82.94 (n)
lizard
(Anolis carolinensis)
Reptilia SMG1 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smg1 33
  • 77.25 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.23554 33
zebrafish
(Danio rerio)
Actinopterygii smg1 33 34
  • 68.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta nonC 34
  • 27 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-1 35 34
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TOR2 34
  • 16 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6873 33
Species where no ortholog for SMG1 was found in the sources mined by GeneCards:
  • 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

Variants for SMG1 Gene

Sequence variations from dbSNP and Humsavar for SMG1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
VAR_041650 A breast pleomorphic lobular carcinoma sample
VAR_041656 A breast infiltrating ductal carcinoma sample
VAR_041657 A breast infiltrating ductal carcinoma sample
rs1000005264 -- 18,863,134(+) AGAAG(A/G)CAAGG intron-variant
rs1000005594 -- 18,874,587(+) CAGGC(G/T)GGGCG intron-variant

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

Variant ID Type Subtype PubMed ID
dgv1310n106 CNV deletion 24896259
dgv2787n100 CNV gain 25217958
dgv57e180 CNV deletion 20482838
esv2169089 CNV deletion 18987734
esv22839 CNV gain 19812545
esv2632615 CNV deletion 19546169
esv2666793 CNV deletion 23128226
esv2714043 CNV deletion 23290073
esv2758634 CNV gain+loss 17122850
esv34419 CNV gain 17911159
esv3553196 CNV deletion 23714750
esv3570409 CNV gain 25503493
esv3582070 CNV loss 25503493
esv3638116 CNV loss 21293372
esv3638117 CNV loss 21293372
esv3892806 CNV gain 25118596
esv995185 CNV insertion 20482838
nsv1044846 CNV gain 25217958
nsv1045019 CNV gain 25217958
nsv1047485 CNV gain 25217958
nsv1070995 CNV deletion 25765185
nsv1071274 CNV deletion 25765185
nsv1111126 CNV tandem duplication 24896259
nsv1752 CNV deletion 18451855
nsv1753 CNV insertion 18451855
nsv428320 CNV loss 18775914
nsv436205 CNV deletion 17901297
nsv469598 CNV gain 16826518
nsv512427 CNV loss 21212237
nsv571579 CNV gain 21841781
nsv571580 CNV gain 21841781
nsv571581 CNV gain 21841781
nsv833161 CNV loss 17160897
nsv9385 CNV loss 18304495
nsv9386 CNV loss 18304495
nsv958168 CNV deletion 24416366
nsv978103 CNV duplication 23825009
nsv984285 CNV duplication 23825009

Variation tolerance for SMG1 Gene

Residual Variation Intolerance Score: 0.265% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.87; 74.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMG1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMG1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMG1 Gene

Disorders for SMG1 Gene

Relevant External Links for SMG1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMG1

No disorders were found for SMG1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 AP (The Journal of biological chemistry 2001) 2 3 4 22 60
  2. AAA+ proteins RUVBL1 and RUVBL2 coordinate PIKK activity and function in nonsense-mediated mRNA decay. (PMID: 20371770) Izumi N … Ohno S (Science signaling 2010) 3 4 22 60
  3. 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 & development 2009) 3 4 22 60
  4. 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 (The Journal of biological chemistry 2007) 2 3 22 60
  5. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PMID: 12554878) Chiu SY … Maquat LE (RNA (New York, N.Y.) 2003) 3 4 22 60

Products for SMG1 Gene

Sources for SMG1 Gene

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