SMG5

SMG5 nonsense mediated mRNA decay factor | EST1B, KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5

SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]

Member of: DE-5 Developmental clusters: GC1

Biological processes 22 terms

cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic ribonucleoprotein granule (GO:0036464)cytosol (GO:0005829)histone deacetylase binding (GO:0042826)mRNA export from nucleus (GO:0006406)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)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein phosphatase 2A binding (GO:0051721)regulation of dephosphorylation (GO:0035303)regulation of telomere maintenance (GO:0032204)regulation of telomere maintenance via telomerase (GO:0032210)telomerase RNA binding (GO:0070034)telomerase RNA binding (GO:0070034)telomerase holoenzyme complex (GO:0005697)telomeric repeat DNA binding (GO:0042162)telomeric repeat DNA binding (GO:0042162)ubiquitin protein ligase binding (GO:0031625)

Expression (TPM)

TFs regulating SMG5 0 TFs

Transcription factors with Perturb-seq knockdown data for SMG5. 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 = SMG5 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 SMG5

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SMG5, 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
chr1:156,020,469–156,021,128	261.9 kb	Distal (>10kb) Multiome	558
chr1:156,052,923–156,055,358	228.0 kb	Distal (>10kb) Multiome	1053
chr1:156,060,806–156,061,738	221.6 kb	Distal (>10kb) Multiome	318
chr1:156,063,507–156,064,184	219.0 kb	Distal (>10kb) Multiome	199
chr1:156,076,488–156,077,355	205.8 kb	Distal (>10kb) Multiome	246
chr1:156,081,942–156,083,586	200.2 kb	Distal (>10kb) Multiome	670
chr1:156,105,879–156,107,316	176.3 kb	Distal (>10kb) Multiome	663
chr1:156,114,184–156,115,669	168.1 kb	Distal (>10kb) Multiome	824
chr1:156,123,520–156,124,091	159.0 kb	Distal (>10kb) Multiome	679
chr1:156,129,945–156,130,610	152.4 kb	Distal (>10kb) Multiome	733
chr1:156,146,058–156,146,760	136.5 kb	Distal (>10kb) Multiome	429
chr1:156,149,593–156,150,242	132.8 kb	Distal (>10kb) Multiome	194
chr1:156,160,602–156,161,218	121.7 kb	Distal (>10kb) Multiome	218
chr1:156,181,487–156,182,119	101.1 kb	Distal (>10kb) Multiome	145
chr1:156,184,002–156,185,155	98.4 kb	Distal (>10kb) Multiome	216
chr1:156,193,531–156,194,375	88.9 kb	Distal (>10kb) Multiome	751
chr1:156,212,611–156,213,686	69.7 kb	Distal (>10kb) Multiome	893
chr1:156,245,413–156,246,269	37.1 kb	Distal (>10kb) Multiome	380
chr1:156,282,165–156,283,323	29 bp	At TSS Multiome	973
chr1:156,291,233–156,291,857	8.7 kb	Proximal (<10kb) Multiome	518
chr1:156,337,825–156,339,056	55.7 kb	Distal (>10kb) Multiome	836
chr1:156,356,873–156,357,393	74.3 kb	Distal (>10kb) Multiome	506
chr1:156,368,893–156,369,552	86.4 kb	Distal (>10kb) Multiome	529
chr1:156,420,712–156,422,291	138.9 kb	Distal (>10kb) Multiome	569
chr1:156,429,277–156,430,847	147.1 kb	Distal (>10kb) Multiome	231
chr1:156,432,112–156,432,986	149.8 kb	Distal (>10kb) Multiome	50
chr1:156,439,076–156,440,265	157.1 kb	Distal (>10kb) Multiome	264
chr1:156,456,348–156,457,982	173.9 kb	Distal (>10kb) Multiome	1033
chr1:156,499,927–156,501,599	218.1 kb	Distal (>10kb) Multiome	950
chr1:156,504,626–156,505,685	222.5 kb	Distal (>10kb) Multiome	911
chr1:156,572,298–156,572,749	289.7 kb	Distal (>10kb) Multiome	580

Genome Browser

Genomic view of the SMG5 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.