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SMG7 SMG7, nonsense mediated mRNA decay factor [ Homo sapiens (human) ]

Gene ID: 9887, updated on 8-Dec-2018

Summary

Official Symbol
SMG7provided by HGNC
Official Full Name
SMG7, nonsense mediated mRNA decay factorprovided by HGNC
Primary source
HGNC:HGNC:16792
See related
Ensembl:ENSG00000116698 MIM:610964
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
EST1C; SGA56M; C1orf16
Summary
This gene encodes a protein that is essential for nonsense-mediated mRNA decay (NMD); a process whereby transcripts with premature termination codons are targeted for rapid degradation by a mRNA decay complex. The mRNA decay complex consists, in part, of this protein along with proteins SMG5 and UPF1. The N-terminal domain of this protein is thought to mediate its association with SMG5 or UPF1 while the C-terminal domain interacts with the mRNA decay complex. This protein may therefore couple changes in UPF1 phosphorylation state to the degradation of NMD-candidate transcripts. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in testis (RPKM 30.4), bone marrow (RPKM 12.9) and 25 other tissues See more
Orthologs

Genomic context

See SMG7 in Genome Data Viewer
Location:
1q25.3
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (183471993..183554193)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183441506..183523328)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nicotinamide nucleotide adenylyltransferase 2 Neighboring gene ribosomal protein S3a pseudogene 8 Neighboring gene uncharacterized LOC105371646 Neighboring gene SMG7 antisense RNA 1 Neighboring gene chromosome 18 open reading frame 32 pseudogene Neighboring gene neutrophil cytosolic factor 2 Neighboring gene uncharacterized LOC107985235

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 Apr 4 07:08:55 2018

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

  • FLJ23717, KIAA0250

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein phosphatase 2A binding IDA
Inferred from Direct Assay
more info
PubMed 
telomerase RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomeric DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomeric DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RNA phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS
Traceable Author Statement
more info
PubMed 
regulation of dephosphorylation TAS
Traceable Author Statement
more info
PubMed 
regulation of telomere maintenance via telomerase IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomere maintenance via telomerase IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
telomerase holoenzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
protein SMG7
Names
EST1 telomerase component homolog C
EST1-like protein C
breast cancer-associated antigen SGA-56M
ever shorter telomeres 1C
smg-7 homolog, nonsense mediated mRNA decay factor
NP_001167532.1
NP_001317936.1
NP_001337148.1
NP_001337149.1
NP_001337150.1
NP_001337151.1
NP_775179.1
NP_963862.1
NP_963863.2
XP_005245706.1
XP_005245709.1
XP_005245710.1
XP_006711741.1
XP_011508507.1
XP_011508508.1
XP_011508509.1
XP_011508510.1
XP_011508511.1
XP_011508512.1
XP_016858457.1
XP_016858458.1
XP_016858459.1

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.

Genomic

  1. NG_029808.1 RefSeqGene

    Range
    5001..86823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001174061.1NP_001167532.1  protein SMG7 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. This variant also contains an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AB085674, AK299178, CN479993, DB223038
    Consensus CDS
    CCDS53445.1
    UniProtKB/Swiss-Prot
    Q92540
    Related
    ENSP00000426915.1, ENST00000508461.5
    Conserved Domains (3) summary
    sd00006
    Location:112138
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:129389
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:13125
    EST1; Telomerase activating protein Est1
  2. NM_001331007.1NP_001317936.1  protein SMG7 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence, uses an alternate in-frame splice junction, and contains an alternate in-frame exon compared to variant 1. The resulting isoform (6) has a longer and distinct N-terminus, contains an alternate internal segment, and lacks another alternate internal segment compared to isoform 1. Variants 6 and 9 encode the same protein (isoform 6).
    Source sequence(s)
    AL137800, AL449223
    Consensus CDS
    CCDS81410.1
    UniProtKB/TrEMBL
    E9PD50
    Related
    ENSP00000356507.3, ENST00000367537.7
    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  3. NM_001350219.1NP_001337148.1  protein SMG7 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AB085674, AL137800, CN479993, D87437, DB223038, DC341780
    Conserved Domains (4) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
    cl26464
    Location:581883
    Atrophin-1; Atrophin-1 family
  4. NM_001350220.1NP_001337149.1  protein SMG7 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AB085674, AL137800, CN479993, CR995963, D87437, DA057117, DA238539, DB223038, DC341780
    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  5. NM_001350221.1NP_001337150.1  protein SMG7 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AB085674, AL137800, CN479993, D87437, DA096344, DB223038, DC341780
    Consensus CDS
    CCDS81410.1
    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  6. NM_001350222.1NP_001337151.1  protein SMG7 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AB085674, AK299178, BC036381, CN479993, DA629659, DA773831, DB223038
    Conserved Domains (1) summary
    pfam10373
    Location:196
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  7. NM_173156.2NP_775179.1  protein SMG7 isoform 1

    See identical proteins and their annotated locations for NP_775179.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AB085674, AY386363, CN479993, DB223038, DC380923
    Consensus CDS
    CCDS1355.1
    UniProtKB/Swiss-Prot
    Q92540
    UniProtKB/TrEMBL
    Q6TV06
    Related
    ENSP00000340766.2, ENST00000347615.6
    Conserved Domains (3) summary
    sd00006
    Location:154180
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:171431
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:55167
    EST1; Telomerase activating protein Est1
  8. NM_201568.2NP_963862.1  protein SMG7 isoform 2

    See identical proteins and their annotated locations for NP_963862.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AB085674, CN479993, D87437, DB223038, DC380923
    Consensus CDS
    CCDS53444.1
    UniProtKB/Swiss-Prot
    Q92540
    Related
    ENSP00000421358.2, ENST00000515829.6
    Conserved Domains (3) summary
    sd00006
    Location:154180
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:171431
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:55167
    EST1; Telomerase activating protein Est1
  9. NM_201569.2NP_963863.2  protein SMG7 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 4) has a distinct C-terminus and is longer than isoform 1.
    Source sequence(s)
    AB085674, AK299178, AL137800, BC036381, CN479993, DB223038
    Consensus CDS
    CCDS41445.2
    UniProtKB/Swiss-Prot
    Q92540
    Related
    ENSP00000425133.1, ENST00000507469.5
    Conserved Domains (3) summary
    sd00006
    Location:154180
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:171431
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:55167
    EST1; Telomerase activating protein Est1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    183471993..183554193
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510205.3XP_011508507.1  protein SMG7 isoform X1

    See identical proteins and their annotated locations for XP_011508507.1

    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  2. XM_011510209.3XP_011508511.1  protein SMG7 isoform X7

    Conserved Domains (4) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
    cl26464
    Location:581883
    Atrophin-1; Atrophin-1 family
  3. XM_011510206.3XP_011508508.1  protein SMG7 isoform X3

    See identical proteins and their annotated locations for XP_011508508.1

    UniProtKB/TrEMBL
    E9PD50
    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  4. XM_011510207.3XP_011508509.1  protein SMG7 isoform X4

    See identical proteins and their annotated locations for XP_011508509.1

    Conserved Domains (3) summary
    sd00006
    Location:136162
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:153413
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:37149
    EST1; Telomerase activating protein Est1
  5. XM_005245649.4XP_005245706.1  protein SMG7 isoform X1

    See identical proteins and their annotated locations for XP_005245706.1

    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  6. XM_011510208.3XP_011508510.1  protein SMG7 isoform X5

    Conserved Domains (3) summary
    sd00006
    Location:183209
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:200460
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:84196
    EST1; Telomerase activating protein Est1
  7. XM_017002969.1XP_016858458.1  protein SMG7 isoform X10

    Conserved Domains (2) summary
    pfam09606
    Location:351521
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam10373
    Location:196
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  8. XM_017002970.1XP_016858459.1  protein SMG7 isoform X10

    Conserved Domains (2) summary
    pfam09606
    Location:351521
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam10373
    Location:196
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  9. XM_011510210.2XP_011508512.1  protein SMG7 isoform X8

    Conserved Domains (3) summary
    sd00006
    Location:112138
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:129389
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:13125
    EST1; Telomerase activating protein Est1
  10. XM_017002968.2XP_016858457.1  protein SMG7 isoform X9

  11. XM_005245652.3XP_005245709.1  protein SMG7 isoform X2

    Conserved Domains (3) summary
    sd00006
    Location:154180
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:171431
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:55167
    EST1; Telomerase activating protein Est1
  12. XM_006711678.3XP_006711741.1  protein SMG7 isoform X6

    See identical proteins and their annotated locations for XP_006711741.1

    Conserved Domains (3) summary
    sd00006
    Location:154180
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:171431
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:55167
    EST1; Telomerase activating protein Est1
  13. XM_005245653.5XP_005245710.1  protein SMG7 isoform X4

    See identical proteins and their annotated locations for XP_005245710.1

    Conserved Domains (3) summary
    sd00006
    Location:136162
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:153413
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:37149
    EST1; Telomerase activating protein Est1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014837.3: Suppressed sequence

    Description
    NM_014837.3: This RefSeq was permanently suppressed because it has a non-consensus splice site that does't have any mRNA support.
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