Human Gene SMG6 (uc002fub.1) Description and Page Index
Description: Homo sapiens smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans) (SMG6), transcript variant 1, mRNA. RefSeq Summary (NM_017575): 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]. Transcript (Including UTRs) Position: hg19 chr17:1,963,133-2,207,069 Size: 243,937 Total Exon Count: 19 Strand: - Coding Region Position: hg19 chr17:1,964,786-2,207,014 Size: 242,229 Coding Exon Count: 19
ID:EST1A_HUMAN DESCRIPTION: RecName: Full=Telomerase-binding protein EST1A; EC=3.1.-.-; AltName: Full=EST1-like protein A; AltName: Full=Ever shorter telomeres 1A; AltName: Full=Smg-6 homolog; AltName: Full=Telomerase subunit EST1A; AltName: Full=hSmg5/7a; 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). 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. COFACTOR: Manganese. SUBUNIT: 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 PP2A catalytic subunits, SMG1, UPF1, UPF2 and UPF3B. INTERACTION: Q92900-2:UPF1; NbExp=2; IntAct=EBI-3232100, EBI-373492; SUBCELLULAR LOCATION: Nucleus, nucleolus. Chromosome, telomere (Probable). Cytoplasm, cytosol. Note=Particularly enriched in the nucleolus. TISSUE SPECIFICITY: Ubiquitous. DOMAIN: The PINc domain confers endonuclease activity and is expected to bind the catalytic metal ion. SIMILARITY: Contains 1 PINc domain. SEQUENCE CAUTION: Sequence=AAH64916.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA34452.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Genetic Association Studies of Complex Diseases and Disorders
Aorta Ramachandran S Vasan et al. JAMA : the journal of the American Medical Association 2009, Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data., JAMA : the journal of the American Medical Association.
We identified 5 genetic loci harboring common variants that were associated with variation in LV diastolic dimensions and aortic root size, but such findings explained a very small proportion of variance. Further studies are required to replicate these findings, identify the causal variants at or near these loci, characterize their functional significance, and determine whether they are related to overt cardiovascular disease.
Aortic root size Vasan ,et al. 2009, Genetic Variants Associated with Cardiac Structure and Function: A Meta-analysis and Replication of Genome-wide Association Data, JAMA 2009 302- 2 : 168-78.
We identified 5 genetic loci harboring common variants that were associated with variation in LV diastolic dimensions and aortic root size, but such findings explained a very small proportion of variance.
Coronary Artery Disease Heribert Schunkert et al. Nature genetics 2011, Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease., Nature genetics.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q86US8
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.