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

Summary

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

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
SMG1 and CDK12 Link DeltaNp63alpha Phosphorylation to RNA Surveillance in Keratinocytes.
Title: SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes.
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.
Cryo-EM structure of SMG1-SMG8-SMG9 complex.
Title: Cryo-EM structure of SMG1-SMG8-SMG9 complex.
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.
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.
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.
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.
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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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S3056 (e-PCR)
- UniSTS:29449

D11S2921 (e-PCR)
- UniSTS:152074

RH66032 (e-PCR)
- UniSTS:6682

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

RH65949 (e-PCR)
- UniSTS:90973

RH68916 (e-PCR)
- UniSTS:11623

RH121406 (e-PCR)
- UniSTS:134253

RH102308 (e-PCR)
- UniSTS:96642

SHGC-37696 (e-PCR)
- UniSTS:31894

SHGC-110958 (e-PCR)
- UniSTS:168105

D16S3241 (e-PCR)
- UniSTS:21201

SMG1 (e-PCR)
- UniSTS:504801

SHGC-149218 (e-PCR)
- UniSTS:176869

SMG1_1253 (e-PCR)
- UniSTS:277754

SMG1_v362 (e-PCR)
- UniSTS:277754

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables diacylglycerol-dependent serine/threonine kinase activity	EXP Inferred from Experiment more info	PubMed
enables histone H2AS1 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 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

EC 2.7.11.1

XP_005255239.1

EC 2.7.11.1

XP_005255240.1

EC 2.7.11.1

XP_005255241.1

EC 2.7.11.1

XP_011544071.1

EC 2.7.11.1

XP_011544072.1

EC 2.7.11.1

XP_016878555.1

EC 2.7.11.1

XP_016878556.1

EC 2.7.11.1

XP_024305967.1

EC 2.7.11.1

XP_047289748.1

EC 2.7.11.1

XP_047289749.1

EC 2.7.11.1

XP_047289750.1

EC 2.7.11.1

XP_047289751.1

EC 2.7.11.1

XP_047289752.1

EC 2.7.11.1

XP_054235809.1

EC 2.7.11.1

XP_054235810.1

EC 2.7.11.1

XP_054235811.1

EC 2.7.11.1

XP_054235812.1

EC 2.7.11.1

XP_054235813.1

EC 2.7.11.1

XP_054235814.1

EC 2.7.11.1

XP_054235815.1

EC 2.7.11.1

XP_054235816.1

EC 2.7.11.1

XP_054235817.1

EC 2.7.11.1

XP_054235818.1

EC 2.7.11.1

XP_054235819.1

EC 2.7.11.1

XP_054235820.1

EC 2.7.11.1

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)

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

18804860..18926408 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Related

ENSP00000456259.1, ENST00000565324.5
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
XM_047433793.1 → XP_047289749.1 serine/threonine-protein kinase SMG1 isoform X4
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
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
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
XM_047433794.1 → XP_047289750.1 serine/threonine-protein kinase SMG1 isoform X6
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
XM_047433795.1 → XP_047289751.1 serine/threonine-protein kinase SMG1 isoform X7
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
XM_047433792.1 → XP_047289748.1 serine/threonine-protein kinase SMG1 isoform X3
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
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