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

Gene ID: 23049, updated on 2-Oct-2018

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; Vega:OTTHUMG00000166900
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

Genomic context

See SMG1 in Genome Data Viewer
Location:
16p12.3
Exon count:
65
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (18804853..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

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystem (from REACTOME)
    Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC), organism-specific biosystemDuring normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of trans...
  • Nonsense-Mediated Decay (NMD), organism-specific biosystem (from REACTOME)
    Nonsense-Mediated Decay (NMD), organism-specific biosystemThe Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. ...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
Component Evidence Code Pubs
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

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)

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_015092.4NP_055907.3  serine/threonine-protein kinase SMG1

    See identical proteins and their annotated locations for NP_055907.3

    Status: REVIEWED

    Source sequence(s)
    AB061371, AK025794, AL833298, AW088221, AW503964, AY014957, BC037335, BE079340, DA433527, DA854035
    Consensus CDS
    CCDS45430.1
    UniProtKB/Swiss-Prot
    Q96Q15
    Related
    ENSP00000402515.2, OTTHUMP00000234388, ENST00000446231.6, OTTHUMT00000391817
    Conserved Domains (3) summary
    cd05170
    Location:21212426
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36313660
    FATC; FATC domain
    pfam15785
    Location:6311242
    SMG1; Serine/threonine-protein kinase smg-1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    18804853..18926428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255183.4XP_005255240.1  serine/threonine-protein kinase SMG1 isoform X3

    Conserved Domains (3) summary
    cd05170
    Location:20952428
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36333662
    FATC; FATC domain
    pfam15785
    Location:6051216
    SMG1; Serine/threonine-protein kinase smg-1
  2. XM_005255184.4XP_005255241.1  serine/threonine-protein kinase SMG1 isoform X4

    Related
    OTTHUMP00000256093
    Conserved Domains (3) summary
    cd05170
    Location:20692402
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36073636
    FATC; FATC domain
    pfam15785
    Location:5791190
    SMG1; Serine/threonine-protein kinase smg-1
  3. XM_011545769.3XP_011544071.1  serine/threonine-protein kinase SMG1 isoform X2

    Conserved Domains (3) summary
    cd05170
    Location:21212454
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36583687
    FATC; FATC domain
    pfam15785
    Location:6311242
    SMG1; Serine/threonine-protein kinase smg-1
  4. XM_024450198.1XP_024305966.1  serine/threonine-protein kinase SMG1 isoform X5

    Conserved Domains (3) summary
    cd05170
    Location:20432376
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:35813610
    FATC; FATC domain
    pfam15785
    Location:5531162
    SMG1; Serine/threonine-protein kinase smg-1
  5. XM_005255182.3XP_005255239.1  serine/threonine-protein kinase SMG1 isoform X1

    Conserved Domains (3) summary
    cd05170
    Location:21212454
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36593688
    FATC; FATC domain
    pfam15785
    Location:6311242
    SMG1; Serine/threonine-protein kinase smg-1
  6. XM_024450199.1XP_024305967.1  serine/threonine-protein kinase SMG1 isoform X5

    Related
    ENSP00000456259.1, ENST00000565324.5
    Conserved Domains (3) summary
    cd05170
    Location:20432376
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:35813610
    FATC; FATC domain
    pfam15785
    Location:5531162
    SMG1; Serine/threonine-protein kinase smg-1
  7. XM_017023066.2XP_016878555.1  serine/threonine-protein kinase SMG1 isoform X3

    Conserved Domains (3) summary
    cd05170
    Location:20952428
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:36333662
    FATC; FATC domain
    pfam15785
    Location:6051216
    SMG1; Serine/threonine-protein kinase smg-1
  8. XM_011545770.1XP_011544072.1  serine/threonine-protein kinase SMG1 isoform X6

    Conserved Domains (3) summary
    cd05170
    Location:14911824
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:30293058
    FATC; FATC domain
    pfam15785
    Location:1612
    SMG1; Serine/threonine-protein kinase smg-1
  9. XM_017023067.1XP_016878556.1  serine/threonine-protein kinase SMG1 isoform X6

    Conserved Domains (3) summary
    cd05170
    Location:14911824
    PIKKc_SMG1; Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1
    pfam02260
    Location:30293058
    FATC; FATC domain
    pfam15785
    Location:1612
    SMG1; Serine/threonine-protein kinase smg-1
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