Gene Page: SMG5

Summary ?
GeneID23381
SymbolSMG5
SynonymsEST1B|LPTS-RP1|LPTSRP1|SMG-5
DescriptionSMG5 nonsense mediated mRNA decay factor
ReferenceMIM:610962|HGNC:HGNC:24644|Ensembl:ENSG00000198952|HPRD:16869|Vega:OTTHUMG00000017491
Gene typeprotein-coding
Map location1q21.2
Sherlock p-value0.031
Fetal beta-0.375

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
GSMA_IGenome scan meta-analysisPsr: 0.0235 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00814 

Section I. Genetics and epigenetics annotation


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
GenePearson's Correlation Spearman's Correlation
NID20.810.52
SLC26A20.760.52
COL3A10.760.34
NID10.760.45
COL6A30.760.19
CD930.740.46
FBN20.740.55
COL4A10.730.46
COL1A20.730.29
SLC6A40.720.34
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.37-0.47
AF347015.31-0.35-0.51
MT-CO2-0.35-0.52
AF347015.27-0.34-0.50
AF347015.33-0.34-0.49
ASPHD1-0.34-0.34
MT-CYB-0.34-0.49
HLA-F-0.34-0.38
AF347015.8-0.34-0.50
CXCL14-0.33-0.49

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI12699629 |14636577 
GO:0051721protein phosphatase 2A bindingIDA14636577 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decayTAS16488880 
GO:0006406mRNA export from nucleusTAS16488880 
GO:0035303regulation of dephosphorylationIMP14636577 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIDA14636577 
GO:0005737cytoplasmIDA14636577 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID HDAC CLASSI PATHWAY 6650All SZGR 2.0 genes in this pathway
PID TELOMERASE PATHWAY 6848All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA 284128All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330155All SZGR 2.0 genes in this pathway
REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 17657All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP 290177All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335193All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
LIAO HAVE SOX4 BINDING SITES 4026All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539324All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290172All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH3 21 UP 4430All SZGR 2.0 genes in this pathway
HU GENOTOXIC DAMAGE 4HR 3528All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393244All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022619All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR DN 354216All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 7 7646All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080713All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-433-3p103910461A,m8hsa-miR-433brainAUCAUGAUGGGCUCCUCGGUGU