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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
  • Chromosome 17 Open Reading Frame 31 2
  • EST1 Telomerase Component Homolog A 3
  • EST1-Like Protein A 4
  • Smg-6 Homolog 4
  • EC 3.1.2.15 63
  • EC 3.1.-.- 4
  • EC 3.1.13 63
  • 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. Among its related pathways are mRNA surveillance pathway and Gene Expression. 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around SMG6 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for SMG6 Gene at MOPED

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:0070182 DNA polymerase binding IPI 15857955
genes like me logo Genes that share ontologies with SMG6: view
genes like me logo Genes that share phenotypes with SMG6: view

Animal Model Products

miRNA for SMG6 Gene

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , 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: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:0006406 mRNA export from nucleus TAS 16488880
GO:0010467 gene expression TAS --
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
Grn163l Investigational Pharma Target 0
Manganese Pharma 32
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:

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, MOPED, and MaxQB for SMG6 Gene



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

Protein tissue co-expression partners for SMG6 Gene

Primer Products

In Situ Assay 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
cow
(Bos Taurus)
Mammalia SMG6 35
  • 91.33 (n)
  • 92.7 (a)
SMG6 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMG6 35
  • 91.67 (n)
  • 93.2 (a)
SMG6 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smg6 35
  • 88.5 (n)
  • 90.9 (a)
Smg6 16
Smg6 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SMG6 35
  • 98.85 (n)
  • 98.38 (a)
SMG6 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smg6 35
  • 88.36 (n)
  • 91.4 (a)
oppossum
(Monodelphis domestica)
Mammalia SMG6 36
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMG6 36
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC101750600 35
  • 72.96 (n)
  • 73.13 (a)
SMG6 36
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMG6 36
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smg6 35
  • 65.68 (n)
  • 66.15 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100334020 35
  • 62.45 (n)
  • 63.63 (a)
smg6 36
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Smg6 36
  • 28 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smg-6 36
  • 19 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 52 (a)
OneToMany
-- 36
  • 39 (a)
OneToMany
Species with no ortholog for SMG6:
  • 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
rs1885986 - 2,299,881(-) GCCAC(C/G)ACTGA reference, missense
rs216195 - 2,299,873(-) TGAAG(A/C)AGCAA reference, missense
rs1885987 - 2,299,731(-) GAAAA(A/C)CAGTG reference, missense
VAR_018502 -
rs2273980 - 2,068,915(-) GGACC(A/G)CAGTC reference, missense

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

Variant ID Type Subtype PubMed ID
nsv907523 CNV Loss 21882294
nsv827857 CNV Gain 20364138
dgv3035n71 CNV Loss 21882294
esv2668978 CNV Deletion 23128226
nsv519347 CNV Loss 19592680
esv2715491 CNV Deletion 23290073
esv2715492 CNV Deletion 23290073
esv2715493 CNV Deletion 23290073
esv2715494 CNV Deletion 23290073
nsv833336 CNV Loss 17160897
nsv469765 CNV Complex 16826518
esv275569 CNV Loss 21479260
esv27421 CNV Loss 19812545
esv2715495 CNV Deletion 23290073
esv2050174 CNV Deletion 18987734
esv3071 CNV Deletion 18987735
esv2715497 CNV Deletion 23290073
esv1259463 CNV Deletion 17803354
esv2715498 CNV Deletion 23290073
esv2715499 CNV Deletion 23290073
esv2715500 CNV Deletion 23290073

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

HapMap Linkage Disequilibrium report
SMG6
Human Gene Mutation Database (HGMD)
SMG6

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

Disorders for SMG6 Gene

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

No disorders were found for SMG6 Gene.

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

Publications for SMG6 Gene

  1. Functional conservation of the telomerase protein Est1p in humans. (PMID: 12699629) Snow B.E. … Harrington L. (Curr. Biol. 2003) 2 3 4 67
  2. 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 23
  3. SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. (PMID: 15721257) Fukuhara N. … Conti E. (Mol. Cell 2005) 3 23
  4. 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
  5. Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. (PMID: 25429978) Schmidt S.A. … Green P.J. (Nucleic Acids Res. 2015) 3

Products for SMG6 Gene

Sources for SMG6 Gene

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