Format

Send to:

Choose Destination

SMG6 SMG6, nonsense mediated mRNA decay factor [ Homo sapiens (human) ]

Gene ID: 23293, updated on 12-Aug-2018

Summary

Official Symbol
SMG6provided by HGNC
Official Full Name
SMG6, nonsense mediated mRNA decay factorprovided by HGNC
Primary source
HGNC:HGNC:17809
See related
Ensembl:ENSG00000070366 MIM:610963; Vega:OTTHUMG00000177578
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
EST1A; SMG-6; C17orf31; hSMG5/7a
Summary
This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]
Expression
Ubiquitous expression in ovary (RPKM 7.3), testis (RPKM 5.9) and 25 other tissues See more
Orthologs

Genomic context

See SMG6 in Genome Data Viewer
Location:
17p13.3
Exon count:
30
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (2059839..2303836, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1963133..2207069, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984988 Neighboring gene microRNA 212 Neighboring gene HIC ZBTB transcriptional repressor 1 Neighboring gene MCUR1 pseudogene 1 Neighboring gene VISTA enhancer hs1445 Neighboring gene VISTA enhancer hs924 Neighboring gene RNA, 7SL, cytoplasmic 624, pseudogene Neighboring gene heart enhancer 8 Neighboring gene uncharacterized LOC101927839 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 16 Neighboring gene serine racemase Neighboring gene small nucleolar RNA, C/D box 91B Neighboring gene TSR1, ribosome maturation factor

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?

Phenotypes

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data.
NHGRI GWA Catalog
Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.
NHGRI GWA Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
NHGRI GWA Catalog
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with smg-6 homolog, nonsense mediated mRNA decay factor (SMG6; EST1A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

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. ...
  • Regulation of Telomerase, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of Telomerase, organism-specific biosystem
    Regulation of Telomerase
  • 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

  • FLJ35688, KIAA0732

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA polymerase binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
endoribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
endoribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoribonuclease activity TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomerase RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomerase RNA binding IPI
Inferred from Physical Interaction
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 
Component Evidence Code Pubs
chromosome, telomeric region IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
colocalizes_with exon-exon junction complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
telomerase holoenzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomerase holoenzyme complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
telomerase-binding protein EST1A
Names
EST1 telomerase component homolog A
ever shorter telomeres 1A
smg-6 homolog, nonsense mediated mRNA decay factor
telomerase subunit EST1A
NP_001243756.1
NP_001243757.1
NP_001269255.1
NP_060045.4
XP_005256626.1
XP_005256627.1
XP_005256628.1
XP_011522071.1
XP_011522074.1
XP_011522075.1
XP_011522076.1
XP_011522077.1
XP_016879887.1
XP_016879888.1
XP_024306449.1

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_033980.1 RefSeqGene

    Range
    5001..248937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256827.1NP_001243756.1  telomerase-binding protein EST1A isoform 3

    See identical proteins and their annotated locations for NP_001243756.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate internal promoter and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG, and the resulting isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3 and 4 encode the same protein (isoform 3).
    Source sequence(s)
    AC090617, AL450226, BC064916
    Consensus CDS
    CCDS58498.1
    UniProtKB/Swiss-Prot
    Q86US8
    Related
    ENSP00000346977.4, OTTHUMP00000257227, ENST00000354901.8, OTTHUMT00000438057
    Conserved Domains (2) summary
    cd09885
    Location:333508
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:4195
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  2. NM_001256828.1NP_001243757.1  telomerase-binding protein EST1A isoform 3

    See identical proteins and their annotated locations for NP_001243757.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate internal promoter and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG, and the resulting isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3 and 4 encode the same protein (isoform 3).
    Source sequence(s)
    AC090617, AK302964, AL450226
    Consensus CDS
    CCDS58498.1
    UniProtKB/Swiss-Prot
    Q86US8
    Related
    ENSP00000440283.2, OTTHUMP00000257229, ENST00000536871.6, OTTHUMT00000438059
    Conserved Domains (2) summary
    cd09885
    Location:333508
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:4195
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  3. NM_001282326.1NP_001269255.1  telomerase-binding protein EST1A isoform 4

    See identical proteins and their annotated locations for NP_001269255.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate internal promoter and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at an alternate AUG, and the resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC090617, AL133597, DB333407
    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (1) summary
    cd09885
    Location:152327
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
  4. NM_017575.4NP_060045.4  telomerase-binding protein EST1A isoform 1

    See identical proteins and their annotated locations for NP_060045.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB018275, AC090617, AL450226, AY168921
    Consensus CDS
    CCDS11016.1
    UniProtKB/Swiss-Prot
    Q86US8
    Related
    ENSP00000263073.5, OTTHUMP00000257106, ENST00000263073.10, OTTHUMT00000437826
    Conserved Domains (4) summary
    cd09885
    Location:12411416
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    sd00006
    Location:765795
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:7511103
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:638741
    EST1; Telomerase activating protein Est1

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_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    2059839..2303836 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256571.5XP_005256628.1  telomerase-binding protein EST1A isoform X7

    See identical proteins and their annotated locations for XP_005256628.1

    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (2) summary
    cd09885
    Location:333508
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:4195
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  2. XM_011523769.2XP_011522071.1  telomerase-binding protein EST1A isoform X1

    See identical proteins and their annotated locations for XP_011522071.1

    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (4) summary
    cd09885
    Location:12101385
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:7201072
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:607710
    EST1; Telomerase activating protein Est1
    cl28310
    Location:116307
    Rho; Transcription termination factor Rho [Transcription]
  3. XM_024450681.1XP_024306449.1  telomerase-binding protein EST1A isoform X1

    Conserved Domains (4) summary
    cd09885
    Location:12101385
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:7201072
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:607710
    EST1; Telomerase activating protein Est1
    cl28310
    Location:116307
    Rho; Transcription termination factor Rho [Transcription]
  4. XM_005256569.4XP_005256626.1  telomerase-binding protein EST1A isoform X1

    See identical proteins and their annotated locations for XP_005256626.1

    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (4) summary
    cd09885
    Location:12101385
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:7201072
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:607710
    EST1; Telomerase activating protein Est1
    cl28310
    Location:116307
    Rho; Transcription termination factor Rho [Transcription]
  5. XM_017024399.2XP_016879888.1  telomerase-binding protein EST1A isoform X7

    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (2) summary
    cd09885
    Location:333508
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:4195
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  6. XM_011523775.2XP_011522077.1  telomerase-binding protein EST1A isoform X7

    See identical proteins and their annotated locations for XP_011522077.1

    UniProtKB/Swiss-Prot
    Q86US8
    Conserved Domains (2) summary
    cd09885
    Location:333508
    PIN_Smg6; PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs
    pfam10373
    Location:4195
    EST1_DNA_bind; Est1 DNA/RNA binding domain
  7. XM_011523772.2XP_011522074.1  telomerase-binding protein EST1A isoform X2

    Conserved Domains (3) summary
    sd00006
    Location:765795
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:751957
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:638741
    EST1; Telomerase activating protein Est1
  8. XM_017024398.1XP_016879887.1  telomerase-binding protein EST1A isoform X3

  9. XM_011523774.2XP_011522076.1  telomerase-binding protein EST1A isoform X6

    Conserved Domains (3) summary
    sd00006
    Location:765795
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:751831
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:638741
    EST1; Telomerase activating protein Est1
  10. XM_011523773.2XP_011522075.1  telomerase-binding protein EST1A isoform X4

    Conserved Domains (3) summary
    sd00006
    Location:765795
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:751831
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:638741
    EST1; Telomerase activating protein Est1
  11. XM_005256570.3XP_005256627.1  telomerase-binding protein EST1A isoform X5

    Conserved Domains (3) summary
    sd00006
    Location:765795
    TPR; TPR repeat [structural motif]
    pfam10373
    Location:751831
    EST1_DNA_bind; Est1 DNA/RNA binding domain
    pfam10374
    Location:638741
    EST1; Telomerase activating protein Est1

RNA

  1. XR_001752459.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001170957.1: Suppressed sequence

    Description
    NM_001170957.1: This RefSeq was permanently suppressed because currently there is insufficient support for the full-length exon combination of the transcript.
Support Center