SMG6

SMG6 nonsense mediated mRNA decay factor | EST1A, KIAA0732, SMG-6, C17orf31

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]

Member of: DE-4 Developmental clusters: GC6

Biological processes 32 terms

DNA polymerase binding (GO:0070182)RNA binding (GO:0003723)RNA endonuclease activity (GO:0004521)RNA endonuclease activity (GO:0004521)RNA endonuclease activity (GO:0004521)chromosome, telomeric region (GO:0000781)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)exon-exon junction complex (GO:0035145)mRNA export from nucleus (GO:0006406)negative regulation of telomere capping (GO:1904354)nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleus (GO:0005634)protein binding (GO:0005515)regulation of dephosphorylation (GO:0035303)regulation of telomere maintenance (GO:0032204)regulation of telomere maintenance via telomerase (GO:0032210)regulation of telomere maintenance via telomerase (GO:0032210)ribonucleoprotein complex binding (GO:0043021)telomerase RNA binding (GO:0070034)telomerase RNA binding (GO:0070034)telomerase holoenzyme complex (GO:0005697)telomerase holoenzyme complex (GO:0005697)telomeric repeat DNA binding (GO:0042162)telomeric repeat DNA binding (GO:0042162)

Expression (TPM)

TFs regulating SMG6 0 TFs

Transcription factors with Perturb-seq knockdown data for SMG6. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = SMG6 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to SMG6

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SMG6, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr17:2,023,483–2,024,229	280.0 kb	Distal (>10kb) Multiome	281
chr17:2,024,769–2,026,284	278.3 kb	Distal (>10kb) Multiome	459
chr17:2,029,741–2,030,885	272.9 kb	Distal (>10kb) Multiome	871
chr17:2,041,423–2,042,366	261.9 kb	Distal (>10kb) Multiome	834
chr17:2,048,764–2,051,218	254.7 kb	Distal (>10kb) Multiome	658
chr17:2,053,643–2,054,179	250.0 kb	Distal (>10kb) Multiome	473
chr17:2,054,616–2,055,766	248.7 kb	Distal (>10kb) Multiome	544
chr17:2,058,401–2,059,503	245.0 kb	Distal (>10kb) Multiome	366
chr17:2,302,778–2,304,288	80 bp	At TSS Multiome	770
chr17:2,336,166–2,337,712	32.7 kb	Distal (>10kb) Multiome	896
chr17:2,392,290–2,394,855	89.1 kb	Distal (>10kb) Multiome	788
chr17:2,396,361–2,397,494	93.2 kb	Distal (>10kb) Multiome	546
chr17:2,398,260–2,402,837	95.9 kb	Distal (>10kb) Multiome	1128
chr17:2,511,517–2,512,317	208.1 kb	Distal (>10kb) Multiome	698
chr17:2,592,971–2,594,792	289.8 kb	Distal (>10kb) Multiome	853

Genome Browser

Genomic view of the SMG6 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.