Gene Page:SMG6

Summary?
GeneID 23293
Symbol SMG6
Synonyms C17orf31|EST1A|SMG-6|hSMG5/7a
Description SMG6 nonsense mediated mRNA decay factor
Reference MIM:610963|HGNC:HGNC:17809|Ensembl:ENSG00000070366|HPRD:06502|Vega:OTTHUMG00000177578
Gene type protein-coding
Map location 17p13.3
Pascal p-value 1.769E-8
Sherlock p-value 0.534
Fetal beta 0.452
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search 与精神分裂症Co-occurance柯ywords: schizophrenia,schizophrenic,schizophrenias Click to show details

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs8077351 chr17 2545472 SMG6 23293 0.09 cis

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
NME3 0.75 0.74
HDHD3 0.74 0.74
GAMT 0.72 0.75
PSMG4 0.72 0.72
BOLA1 0.71 0.70
ILVBL 0.71 0.73
POMGNT1 0.70 0.68
NTHL1 0.69 0.71
C9orf142 0.69 0.67
RANGRF 0.69 0.61
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
MT-ATP8 -0.41 -0.48
AF347015.2 -0.40 -0.42
AF347015.15 -0.39 -0.43
AF347015.8 -0.39 -0.43
AF347015.26 -0.39 -0.45
AF347015.18 -0.38 -0.45
COBLL1 -0.38 -0.37
ABCG2 -0.37 -0.41
MT-CYB -0.36 -0.42
CALD1 -0.36 -0.39

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0003677 DNA binding IEA -
GO:0005515 protein binding 新闻学会 12699629
GO:0004519 endonuclease activity IEA -
GO:0016787 hydrolase activity IEA -
GO:0042162 telomeric DNA binding IDA 12699629
GO:0030145 manganese ion binding IEA -
GO:0046872 metal ion binding IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
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:0035303 regulation of dephosphorylation TAS 15721257
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0000781 chromosome, telomeric region IEA -
GO:0005634 nucleus IDA 14636577
GO:0005694 chromosome IEA -
GO:0005697 telomerase holoenzyme complex TAS 12699629
GO:0005737 cytoplasm IDA 14636577

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
PID TELOMERASE PATHWAY 68 48 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA 284 128 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330 155 All SZGR 2.0 genes in this pathway
REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 176 57 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552 347 All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND SERUM DEPRIVATION UP 211 136 All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS G UP 238 135 All SZGR 2.0 genes in this pathway
OLSSON E2F3 TARGETS UP 28 14 All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414 287 All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514 330 All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION 456 287 All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857 456 All SZGR 2.0 genes in this pathway
BILANGES SERUM SENSITIVE VIA TSC2 39 25 All SZGR 2.0 genes in this pathway
TERAO AOX4 TARGETS SKIN UP 38 27 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-199 8 14 m8 hsa-miR-199a CCCAGUGUUCAGACUACCUGUUC
hsa-miR-199b CCCAGUGUUUAGACUAUCUGUUC
miR-299-5p 112 118 1A hsa-miR-299-5p UGGUUUACCGUCCCACAUACAU
miR-7 122 128 1A hsa-miR-7SZ UGGAAGACUAGUGAUUUUGUUG