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Aliases for SMG6 Gene

Aliases for SMG6 Gene

  • SMG6, Nonsense Mediated MRNA Decay Factor 2 3 5
  • Ever Shorter Telomeres 1A 3 4
  • Telomerase Subunit EST1A 3 4
  • HSMG5/7a 3 4
  • C17orf31 3 4
  • EST1A 3 4
  • Smg-6 Homolog, Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • EST1 Telomerase Component Homolog A (S. Cerevisiae) 2
  • Smg-6 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • SMG6 Nonsense Mediated MRNA Decay Factor 2
  • Chromosome 17 Open Reading Frame 31 2
  • EST1 Telomerase Component Homolog A 3
  • Telomerase-Binding Protein EST1A 3
  • EST1-Like Protein A 4
  • Smg-6 Homolog 4
  • EC 3.1.2.15 61
  • EC 3.1.-.- 4
  • EC 3.1.13 61
  • KIAA0732 4
  • SMG-6 3

External Ids for SMG6 Gene

Previous HGNC Symbols for SMG6 Gene

  • C17orf31

Previous GeneCards Identifiers for SMG6 Gene

  • GC17M001910
  • GC17M001916
  • GC17M001920
  • GC17M001924
  • GC17M001926
  • GC17M001929
  • GC17M001963

Summaries for SMG6 Gene

Entrez Gene Summary for SMG6 Gene

  • 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]

GeneCards Summary for SMG6 Gene

SMG6 (SMG6, Nonsense Mediated MRNA Decay Factor) is a Protein Coding gene. Diseases associated with SMG6 include Tricuspid Valve Insufficiency. Among its related pathways are mRNA surveillance pathway and Viral mRNA Translation. GO annotations related to this gene include endoribonuclease activity and telomeric DNA binding. An important paralog of this gene is SMG5.

UniProtKB/Swiss-Prot for SMG6 Gene

  • Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5-(GTGTGG)(4)GTGT-3 telomeric DNA, but not to a telomerase RNA template component (TER).

  • Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA), but not ssDNA or dsRNA.

Gene Wiki entry for SMG6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMG6 Gene

Genomics for SMG6 Gene

Regulatory Elements for SMG6 Gene

Enhancers for SMG6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F001385 0.6 Ensembl ENCODE 41.4 +913.8 913813 9.2 HDGF PKNOX1 ARNT WRNIP1 FEZF1 YBX1 ZNF2 ZNF207 ZNF416 FOS SMYD4 RPA1 SMG6 ENSG00000263345 GEMIN4 HNRNPA1P16 HIC1 CRK SRR ENSG00000262434
GH17F001939 0.5 ENCODE 20.2 +363.6 363623 1.6 ZFP64 ZNF493 ZNF354C ZNF202 ZNF680 REST ZNF518A ZNF623 ZNF781 ZNF843 SMYD4 METTL16 RPA1 HNRNPA1P16 RN7SL608P ENSG00000263345 SMG6 ENSG00000263050 DPH1 HIC1
GH17F002390 0.8 FANTOM5 ENCODE 19.5 -95.2 -95199 18.6 CREB3L1 MLX FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 METTL16 SMYD4 ENSG00000263345 SMG6 MNT EIF4A1P9 SAMD11P1 ENSG00000262869 OR1E3 OR1D2
GH17F001785 1.2 Ensembl ENCODE 17.1 +516.4 516430 3.4 GTF2F1 TBP JUN MAX SIN3A ZIC2 HIC1 ZNF121 ZNF366 SMARCC2 SMYD4 SMG6 SERPINF1 SERPINF2 RPA1 MIR22 MIR22HG WDR81 TLCD2 ENSG00000263345
GH17F002505 0.4 FANTOM5 16.2 -202.2 -202182 0.3 ZNF585B ZNF623 SMG6 HNRNPA1P16 ENSG00000263345 METTL16 ENSG00000263050 GC17P002507 ENSG00000280280 GC17M002465 GC17M002467
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SMG6 on UCSC Golden Path with GeneCards custom track

Promoters for SMG6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001533723 113 2601 ARID4B SIN3A DMAP1 ZNF2 ZNF121 GLIS2 KLF7 ZNF263 SP3 YY2

Genomic Location for SMG6 Gene

Chromosome:
17
Start:
2,059,839 bp from pter
End:
2,303,813 bp from pter
Size:
243,975 bases
Orientation:
Minus strand

Genomic View for SMG6 Gene

Genes around SMG6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMG6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMG6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMG6 Gene

Proteins for SMG6 Gene

  • Protein details for SMG6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86US8-EST1A_HUMAN
    Recommended name:
    Telomerase-binding protein EST1A
    Protein Accession:
    Q86US8
    Secondary Accessions:
    • B7Z874
    • O94837
    • Q86VH6
    • Q9UF60

    Protein attributes for SMG6 Gene

    Size:
    1419 amino acids
    Molecular mass:
    160462 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • May form homooligomers. Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10, NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC). Interacts with TERT, independently of the telomerase RNA. Interacts with SMG1, SMG5, SMG7, UPF1, UPF2, UPF3B and the PP2A catalytic subunits. Also interacts with the exon junction complex (EJC) composed at least of CASC3, EIF4A3, MAGOH and RBM8A; required for the process of nonsense-mediated mRNA decay.
    SequenceCaution:
    • Sequence=AAH64916.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA34452.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SMG6 Gene

    Alternative splice isoforms for SMG6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMG6 Gene

Selected DME Specific Peptides for SMG6 Gene

Post-translational modifications for SMG6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for SMG6 Gene

Suggested Antigen Peptide Sequences for SMG6 Gene

Graphical View of Domain Structure for InterPro Entry

Q86US8

UniProtKB/Swiss-Prot:

EST1A_HUMAN :
  • The PINc domain confers endonuclease activity and is expected to bind the catalytic metal ion.
Domain:
  • The PINc domain confers endonuclease activity and is expected to bind the catalytic metal ion.
  • Contains 1 PINc domain.
genes like me logo Genes that share domains with SMG6: view

No data available for Gene Families for SMG6 Gene

Function for SMG6 Gene

Molecular function for SMG6 Gene

UniProtKB/Swiss-Prot Function:
Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5-(GTGTGG)(4)GTGT-3 telomeric DNA, but not to a telomerase RNA template component (TER).
UniProtKB/Swiss-Prot Function:
Plays a role in nonsense-mediated mRNA decay. Is thought to provide a link to the mRNA degradation machinery as it has endonuclease activity required to initiate NMD, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Degrades single-stranded RNA (ssRNA), but not ssDNA or dsRNA.

Enzyme Numbers (IUBMB) for SMG6 Gene

Gene Ontology (GO) - Molecular Function for SMG6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0004521 endoribonuclease activity TAS --
GO:0005515 protein binding IPI 12699629
genes like me logo Genes that share ontologies with SMG6: view
genes like me logo Genes that share phenotypes with SMG6: view

Animal Models for SMG6 Gene

MGI Knock Outs for SMG6:

Animal Model Products

miRNA for SMG6 Gene

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMG6 Gene

Localization for SMG6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMG6 Gene

Nucleus, nucleolus. Chromosome, telomere. Cytoplasm, cytosol. Note=Particularly enriched in the nucleolus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMG6 Gene COMPARTMENTS Subcellular localization image for SMG6 gene
Compartment Confidence
cytosol 5
nucleus 5
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SMG6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000333 colocalizes_with telomerase catalytic core complex IDA 12676087
GO:0000781 chromosome, telomeric region IEA --
GO:0005634 nucleus IDA 14636577
GO:0005694 chromosome IEA --
GO:0005697 telomerase holoenzyme complex TAS 12699629
genes like me logo Genes that share ontologies with SMG6: view

Pathways & Interactions for SMG6 Gene

genes like me logo Genes that share pathways with SMG6: view

Pathways by source for SMG6 Gene

Gene Ontology (GO) - Biological Process for SMG6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS 16488880
GO:0000723 telomere maintenance IMP 12699629
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0032210 regulation of telomere maintenance via telomerase TAS 16507993
GO:0035303 regulation of dephosphorylation TAS 15721257
genes like me logo Genes that share ontologies with SMG6: view

No data available for SIGNOR curated interactions for SMG6 Gene

Drugs & Compounds for SMG6 Gene

(2) Drugs for SMG6 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 34
Grn163l Investigational Pharma Target 0
genes like me logo Genes that share compounds with SMG6: view

Transcripts for SMG6 Gene

Unigene Clusters for SMG6 Gene

Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMG6 Gene

No ASD Table

Relevant External Links for SMG6 Gene

GeneLoc Exon Structure for
SMG6
ECgene alternative splicing isoforms for
SMG6

Expression for SMG6 Gene

mRNA expression in normal human tissues for SMG6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMG6 Gene

This gene is overexpressed in Adipocyte (20.1), Fetal Brain (12.4), and Testis (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMG6 Gene



Protein tissue co-expression partners for SMG6 Gene

NURSA nuclear receptor signaling pathways regulating expression of SMG6 Gene:

SMG6

SOURCE GeneReport for Unigene cluster for SMG6 Gene:

Hs.448342

mRNA Expression by UniProt/SwissProt for SMG6 Gene:

Q86US8-EST1A_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with SMG6: view

Primer Products

No data available for mRNA differential expression in normal tissues for SMG6 Gene

Orthologs for SMG6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMG6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMG6 34 35
  • 98.85 (n)
dog
(Canis familiaris)
Mammalia SMG6 34 35
  • 91.67 (n)
cow
(Bos Taurus)
Mammalia SMG6 34 35
  • 91.33 (n)
mouse
(Mus musculus)
Mammalia Smg6 34 16 35
  • 88.5 (n)
rat
(Rattus norvegicus)
Mammalia Smg6 34
  • 88.36 (n)
oppossum
(Monodelphis domestica)
Mammalia SMG6 35
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMG6 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC101750600 34
  • 72.96 (n)
SMG6 35
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMG6 35
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smg6 34
  • 65.68 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100334020 34
  • 62.45 (n)
smg6 35
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Smg6 35
  • 28 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smg-6 35
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToMany
-- 35
  • 39 (a)
OneToMany
Species where no ortholog for SMG6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMG6 Gene

ENSEMBL:
Gene Tree for SMG6 (if available)
TreeFam:
Gene Tree for SMG6 (if available)

Paralogs for SMG6 Gene

Paralogs for SMG6 Gene

genes like me logo Genes that share paralogs with SMG6: view

Variants for SMG6 Gene

Sequence variations from dbSNP and Humsavar for SMG6 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1002135 -- 2,194,289(+) ctcaa(G/T)gttct intron-variant, downstream-variant-500B
rs1002136 -- 2,194,712(+) caaaa(A/C)aaaaa intron-variant, utr-variant-3-prime
rs10432015 -- 2,288,815(+) tggct(C/G)acgcc intron-variant
rs10445300 -- 2,211,293(+) TTTAA(C/T)AATAG intron-variant
rs1045524 -- 2,060,976(-) TCCCT(A/G)AGGCC utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SMG6 Gene

Variant ID Type Subtype PubMed ID
esv1259463 CNV deletion 17803354
esv2050174 CNV deletion 18987734
esv2668978 CNV deletion 23128226
esv2715491 CNV deletion 23290073
esv2715492 CNV deletion 23290073
esv2715493 CNV deletion 23290073
esv2715494 CNV deletion 23290073
esv2715495 CNV deletion 23290073
esv2715497 CNV deletion 23290073
esv2715498 CNV deletion 23290073
esv2715499 CNV deletion 23290073
esv2715500 CNV deletion 23290073
esv27421 CNV loss 19812545
esv275569 CNV loss 21479260
esv3071 CNV loss 18987735
esv3572286 CNV gain 25503493
esv3639704 CNV loss 21293372
esv3639705 CNV loss 21293372
esv3639707 CNV loss 21293372
nsv1070109 CNV deletion 25765185
nsv1109040 CNV deletion 24896259
nsv1113840 CNV deletion 24896259
nsv1121522 CNV deletion 24896259
nsv1125189 CNV deletion 24896259
nsv1147173 CNV deletion 26484159
nsv469765 CNV loss 16826518
nsv473277 CNV novel sequence insertion 20440878
nsv475396 CNV novel sequence insertion 20440878
nsv519347 CNV loss 19592680
nsv574216 CNV gain 21841781
nsv574221 CNV loss 21841781
nsv574222 CNV loss 21841781
nsv574223 CNV loss 21841781
nsv574224 CNV gain 21841781
nsv827857 CNV gain 20364138
nsv833336 CNV loss 17160897

Variation tolerance for SMG6 Gene

Residual Variation Intolerance Score: 47.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 22.74; 99.47% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMG6 Gene

Human Gene Mutation Database (HGMD)
SMG6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMG6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMG6 Gene

Disorders for SMG6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SMG6 Gene - From: DISEASES

Disorder Aliases PubMed IDs
tricuspid valve insufficiency
  • tricuspid incompetence
- elite association - COSMIC cancer census association via MalaCards
Search SMG6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SMG6

Genetic Association Database (GAD)
SMG6
Human Genome Epidemiology (HuGE) Navigator
SMG6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMG6
genes like me logo Genes that share disorders with SMG6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SMG6 Gene

Publications for SMG6 Gene

  1. Evidence for association between structural variants in lissencephaly-related genes and executive deficits in schizophrenia or bipolar patients from a Spanish isolate population. (PMID: 19018238) TabarAcs-Seisdedos R. … MartA-nez S. (Psychiatr. Genet. 2008) 3 22 46 64
  2. A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed. (PMID: 12676087) Reichenbach P. … Lingner J. (Curr. Biol. 2003) 2 3 4 64
  3. Functional conservation of the telomerase protein Est1p in humans. (PMID: 12699629) Snow B.E. … Harrington L. (Curr. Biol. 2003) 2 3 4 64
  4. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. (PMID: 21378990) Schunkert H. … Samani N.J. (Nat. Genet. 2011) 3 46 64
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64

Products for SMG6 Gene

Sources for SMG6 Gene

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