Gene Page:SMG5

Summary?
GeneID 23381
Symbol SMG5
Synonyms EST1B|LPTS-RP1|LPTSRP1|SMG-5
Description SMG5 nonsense mediated mRNA decay factor
Reference MIM:610962|HGNC:HGNC:24644|Ensembl:ENSG00000198952|HPRD:16869|Vega:OTTHUMG00000017491
Gene type protein-coding
Map location 1q21.2
Sherlock p-value 0.031
Fetal beta -0.375

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
GSMA_I Genome scan meta-analysis Psr: 0.0235
GSMA_IIA Genome 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
圣1: 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
NID2 0.81 0.52
SLC26A2 0.76 0.52
COL3A1 0.76 0.34
NID1 0.76 0.45
COL6A3 0.76 0.19
CD93 0.74 0.46
FBN2 0.74 0.55
COL4A1 0.73 0.46
COL1A2 0.73 0.29
SLC6A4 0.72 0.34
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005515 protein binding 新闻学会 12699629|14636577
GO:0051721 protein phosphatase 2A binding IDA 14636577
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS 16488880
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0035303 regulation of dephosphorylation IMP 14636577
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005634 nucleus IDA 14636577
GO:0005737 cytoplasm IDA 14636577

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
PID HDAC CLASSI PATHWAY 66 50 All SZGR 2.0 genes in this pathway
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
BASAKI YBX1 TARGETS UP 290 177 All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN 335 193 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
LIAO HAVE SOX4 BINDING SITES 40 26 All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539 324 All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988 594 All SZGR 2.0 genes in this pathway
BENPORATH OCT4 TARGETS 290 172 All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH3 21 UP 44 30 All SZGR 2.0 genes in this pathway
HU GENOTOXIC DAMAGE 4HR 35 28 All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393 244 All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022 619 All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR DN 354 216 All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457 302 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 7 76 46 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080 713 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-433-3p 1039 1046 1A,m8 hsa-miR-433brain AUCAUGAUGGGCUCCUCGGUGU