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

    Gene ID: 9887, updated on 17-Jun-2019

    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
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 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 Neighboring gene Sharpr-MPRA regulatory region 11944

    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
    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_001174061.2NP_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_001331007.2NP_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_001350219.2NP_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_001350220.2NP_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_001350221.2NP_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_001350222.2NP_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_173156.3NP_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_201568.3NP_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_201569.3NP_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.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 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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