Gene Page:PDZRN3

Summary?
GeneID 23024
Symbol PDZRN3
Synonyms LNX3|SEMACAP3|SEMCAP3
Description PDZ domain containing ring finger 3
Reference MIM:609729|HGNC:HGNC:17704|Ensembl:ENSG00000121440|HPRD:15115|Vega:OTTHUMG00000158865
Gene type protein-coding
Map location 3p13
Pascal p-value 0.308
Fetal beta -0.439

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DNM:Ambalavanan_2016 Whole Exome Sequencing This dataset includes 20 de novo mutations detected in 17 COS probands.
GSMA_IIA Genome scan meta-analysis (All samples) Psr: 0.04047
GSMA_IIE Genome scan meta-analysis (European-ancestry samples) Psr: 0.04359

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
PDZRN3 chr3 73651603 C T NM_015009 p.(Asp274Asn) nonsynonymous SNV 0.986 Childhood-onset schizophrenia DNM:Ambalavanan_2016


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
USP24 0.97 0.97
NSD1 0.97 0.97
SMG1 0.96 0.98
BIRC6 0.96 0.98
MED1 0.96 0.97
C10orf18 0.96 0.97
CHD9 0.96 0.98
AFF4 0.95 0.95
NCOA3 0.95 0.96
LRP6 0.95 0.96
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.31 -0.69 -0.84
FXYD1 -0.67 -0.83
MT-CO2 -0.67 -0.84
IFI27 -0.67 -0.83
HIGD1B -0.66 -0.84
AIFM3 -0.66 -0.71
AF347015.27 -0.66 -0.79
HSD17B14 -0.66 -0.75
RAMP1 -0.65 -0.76
TSC22D4 -0.65 -0.73

Section III. Gene Ontology annotation

Molecular function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005515 protein binding IEA -
GO:0008270 zinc ion binding IEA -
GO:0046872 metal ion binding IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
DAVICIONI MOLECULAR ARMS VS ERMS UP 332 228 All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN DN 241 146 All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN 781 465 All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 1781 1082 All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B 392 251 All SZGR 2.0 genes in this pathway
EBAUER TARGETS OF PAX3 FOXO1 FUSION DN 48 31 All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS DN 124 79 All SZGR 2.0 genes in this pathway
KIM MYCN AMPLIFICATION TARGETS UP 92 64 All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546 351 All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 UP 182 119 All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN 261 183 All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP 393 244 All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191 123 All SZGR 2.0 genes in this pathway
阿塞维多甲基化IN LIVER CANCER DN 940 425 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510 309 All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871 505 All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN 546 362 All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE DN 209 137 All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN 277 166 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069 729 All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP 166 105 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE 317 190 All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS DN 229 135 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP 570 339 All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL MATURE DN 99 74 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-330 765 771 m8 hsa-miR-330brain GCAAAGCACACGGCCUGCAGAGA
miR-34/449 389 395 1A hsa-miR-34abrain UGGCAGUGUCUUAGCUGGUUGUU
hsa-miR-34c AGGCAGUGUAGUUAGCUGAUUGC
hsa-miR-449 UGGCAGUGUAUUGUUAGCUGGU
hsa-miR-449b AGGCAGUGUAUUGUUAGCUGGC
miR-381 82 88 1A hsa-miR-381 UAUACAAGGGCAAGCUCUCUGU
miR-433-3p 812 818 m8 hsa-miR-433brain AUCAUGAUGGGCUCCUCGGUGU
miR-486 702 709 1A,m8 hsa-miR-486 UCCUGUACUGAGCUGCCCCGAG
miR-493-5p 700 706 m8 hsa-miR-493-5p UUGUACAUGGUAGGCUUUCAUU
miR-494 445 451 1A hsa-miR-494brain UGAAACAUACACGGGAAACCUCUU