Summary ?
GeneID56136
SymbolPCDHA13
SynonymsCNR5|CNRN5|CNRS5|CRNR5|PCDH-ALPHA13
Descriptionprotocadherin alpha 13
ReferenceMIM:606319|HGNC:HGNC:8667|Ensembl:ENSG00000239389|HPRD:07554|Vega:OTTHUMG00000129614
Gene typeprotein-coding
Map location5q31
Pascal p-value4.383E-5
eGeneAnterior cingulate cortex BA24
Caudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Nucleus accumbens basal ganglia

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
GSMA_IGenome scan meta-analysisPsr: 0.0032 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
PCDHA13chr5140262375CGNM_018900
NM_018901
NM_018902
NM_018903
NM_018904
NM_018905
NM_018906
NM_018907
NM_018908
NM_018909
NM_018910
NM_018911
NM_031411
NM_031849
NM_031857
NM_031860
NM_031865
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
intronic
intronic
intronic
intronic
silent
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
intronic
silent
SchizophreniaDNM:Gulsuner_2013

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs2513585140233942PCDHA13ENSG00000239389.31.175E-60-27851gtex_brain_ba24
rs2513595140233976PCDHA13ENSG00000239389.31.629E-60-27817gtex_brain_ba24
rs2513605140234863PCDHA13ENSG00000239389.38.768E-90-26930gtex_brain_ba24
rs2513615140235076PCDHA13ENSG00000239389.33.123E-60-26717gtex_brain_ba24
rs2513625140236950PCDHA13ENSG00000239389.32.022E-60-24843gtex_brain_ba24
rs2513635140237109PCDHA13ENSG00000239389.38.523E-90-24684gtex_brain_ba24
rs2513645140237387PCDHA13ENSG00000239389.38.928E-90-24406gtex_brain_ba24
rs6301625140237548PCDHA13ENSG00000239389.38.933E-90-24245gtex_brain_ba24
rs2513655140239423PCDHA13ENSG00000239389.38.428E-90-22370gtex_brain_ba24
rs2513665140239786PCDHA13ENSG00000239389.38.428E-90-22007gtex_brain_ba24
rs2513675140240426PCDHA13ENSG00000239389.32.889E-80-21367gtex_brain_ba24
rs715744945140241354PCDHA13ENSG00000239389.31.271E-70-20439gtex_brain_ba24
rs113214795140242451PCDHA13ENSG00000239389.38.428E-90-19342gtex_brain_ba24
rs2513695140242479PCDHA13ENSG00000239389.38.456E-90-19314gtex_brain_ba24
rs2513715140247354PCDHA13ENSG00000239389.38.456E-90-14439gtex_brain_ba24
rs2513745140252935PCDHA13ENSG00000239389.38.885E-90-8858gtex_brain_ba24
rs2513785140257591PCDHA13ENSG00000239389.38.456E-90-4202gtex_brain_ba24
rs2513795140258922PCDHA13ENSG00000239389.39.861E-90-2871gtex_brain_ba24
rs594795140261677PCDHA13ENSG00000239389.31.399E-80-116gtex_brain_ba24
rs2513805140263290PCDHA13ENSG00000239389.31.43E-801497gtex_brain_ba24
rs2513815140264855PCDHA13ENSG00000239389.31.241E-803062gtex_brain_ba24
rs351608905140272255PCDHA13ENSG00000239389.31.265E-8010462gtex_brain_ba24
rs37761215140274310PCDHA13ENSG00000239389.32.1E-7012517gtex_brain_ba24
rs131741195140275674PCDHA13ENSG00000239389.39.809E-9013881gtex_brain_ba24
rs623844845140279665PCDHA13ENSG00000239389.39.807E-9017872gtex_brain_ba24
rs68742185140280425PCDHA13ENSG00000239389.32.612E-8018632gtex_brain_ba24
rs348078945140284031PCDHA13ENSG00000239389.38.885E-9022238gtex_brain_ba24
rs623844885140285179PCDHA13ENSG00000239389.38.885E-9023386gtex_brain_ba24
rs131822285140285674PCDHA13ENSG00000239389.38.885E-9023881gtex_brain_ba24
rs77042235140286119PCDHA13ENSG00000239389.38.885E-9024326gtex_brain_ba24
rs16061225140288401PCDHA13ENSG00000239389.38.885E-9026608gtex_brain_ba24
rs18490545140288787PCDHA13ENSG00000239389.38.885E-9026994gtex_brain_ba24
rs18582965140294163PCDHA13ENSG00000239389.38.885E-9032370gtex_brain_ba24
rs111676555140295566PCDHA13ENSG00000239389.38.885E-9033773gtex_brain_ba24
rs1558045140296749PCDHA13ENSG00000239389.38.885E-9034956gtex_brain_ba24
rs1558035140296871PCDHA13ENSG00000239389.38.885E-9035078gtex_brain_ba24
rs1558015140297521PCDHA13ENSG00000239389.38.885E-9035728gtex_brain_ba24
rs1558005140298378PCDHA13ENSG00000239389.38.885E-9036585gtex_brain_ba24
rs560035140298532PCDHA13ENSG00000239389.38.885E-9036739gtex_brain_ba24
rs560025140298815PCDHA13ENSG00000239389.38.885E-9037022gtex_brain_ba24
rs350059795140299567PCDHA13ENSG00000239389.38.885E-9037774gtex_brain_ba24
rs1558175140301236PCDHA13ENSG00000239389.38.885E-9039443gtex_brain_ba24
rs1558185140302162PCDHA13ENSG00000239389.38.885E-9040369gtex_brain_ba24
rs61492685140302804PCDHA13ENSG00000239389.31.019E-8041011gtex_brain_ba24
rs1558205140307746PCDHA13ENSG00000239389.39.629E-9045953gtex_brain_ba24
rs1558215140309124PCDHA13ENSG00000239389.38.768E-8047331gtex_brain_ba24
rs3977248615140311045PCDHA13ENSG00000239389.38.765E-9049252gtex_brain_ba24
rs2019559265140312792PCDHA13ENSG00000239389.39.852E-9050999gtex_brain_ba24
rs3977448275140312794PCDHA13ENSG00000239389.38.908E-9051001gtex_brain_ba24
rs1558235140314090PCDHA13ENSG00000239389.33.163E-8052297gtex_brain_ba24
rs1558245140314280PCDHA13ENSG00000239389.38.908E-9052487gtex_brain_ba24
rs1558255140315570PCDHA13ENSG00000239389.37.938E-9053777gtex_brain_ba24
rs2460735140317371PCDHA13ENSG00000239389.31.404E-8055578gtex_brain_ba24
rs590723625140318132PCDHA13ENSG00000239389.31.002E-8056339gtex_brain_ba24
rs1997723235140318137PCDHA13ENSG00000239389.31.379E-7056344gtex_brain_ba24
rs1558165140320019PCDHA13ENSG00000239389.38.924E-9058226gtex_brain_ba24
rs1558155140320519PCDHA13ENSG00000239389.38.929E-9058726gtex_brain_ba24
rs58717545140320871PCDHA13ENSG00000239389.39.179E-9059078gtex_brain_ba24
rs2460685140320997PCDHA13ENSG00000239389.39.117E-9059204gtex_brain_ba24
rs1558145140321593PCDHA13ENSG00000239389.38.961E-9059800gtex_brain_ba24
rs1558135140323876PCDHA13ENSG00000239389.36.06E-9062083gtex_brain_ba24
rs2695535140324709PCDHA13ENSG00000239389.36.341E-9062916gtex_brain_ba24
rs758953015140326216PCDHA13ENSG00000239389.31.292E-6064423gtex_brain_ba24
rs2460405140331136PCDHA13ENSG00000239389.38.931E-9069343gtex_brain_ba24
rs2460395140331337PCDHA13ENSG00000239389.31.46E-6069544gtex_brain_ba24
rs2460155140335575PCDHA13ENSG00000239389.38.162E-9073782gtex_brain_ba24
rs1557995140336168PCDHA13ENSG00000239389.38.768E-8074375gtex_brain_ba24
rs23076945140336545PCDHA13ENSG00000239389.34.264E-8074752gtex_brain_ba24
rs58717565140337437PCDHA13ENSG00000239389.38.713E-9075644gtex_brain_ba24
rs2460045140340821PCDHA13ENSG00000239389.38.976E-9079028gtex_brain_ba24
rs1519885140342818PCDHA13ENSG00000239389.39.426E-9081025gtex_brain_ba24
rs1558125140343372PCDHA13ENSG00000239389.39.456E-9081579gtex_brain_ba24
rs1558115140343598PCDHA13ENSG00000239389.32.213E-8081805gtex_brain_ba24
rs1558085140346712PCDHA13ENSG00000239389.31.584E-8084919gtex_brain_ba24
rs1558075140347053PCDHA13ENSG00000239389.31.679E-8085260gtex_brain_ba24
rs37761145140350545PCDHA13ENSG00000239389.31.27E-6088752gtex_brain_ba24

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
PHF200.970.97
HMG20A0.970.98
CSRNP20.970.97
ZNF5120.960.96
TNPO30.960.96
POLR3A0.960.98
CAPRIN10.960.98
EXOC20.960.97
CTTNBP2NL0.960.96
STAU10.960.97
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FXYD1-0.79-0.92
AF347015.31-0.78-0.91
MT-CO2-0.78-0.92
AIFM3-0.77-0.82
TSC22D4-0.77-0.84
AF347015.33-0.76-0.88
S100B-0.76-0.86
AF347015.27-0.76-0.88
HSD17B14-0.75-0.83
IFI27-0.75-0.88

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005509calcium ion bindingIEA-
GO:0005515protein bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007155cell adhesionIEA-
GO:0007156homophilic cell adhesionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0016021integral to membraneIEA-
GO:0005886plasma membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
SANSOM APC TARGETS DN 366238All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
MIKKELSEN IPS WITH HCP H3K27ME3 10276All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-124/50621942200m8hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC
miR-15/16/195/424/497101510221A,m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
miR-1538418471Ahsa-miR-153UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d22592265m8hsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU
hsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU
miR-181152315301A,m8hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-1855258m8hsa-miR-185brainUGGAGAGAAAGGCAGUUC
hsa-miR-185brainUGGAGAGAAAGGCAGUUC
miR-186791797m8hsa-miR-186CAAAGAAUUCUCCUUUUGGGCUU
miR-197968031A,m8hsa-miR-19aUGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19bUGUGCAAAUCCAUGCAAAACUGA
miR-218179117981A,m8hsa-miR-218brainUUGUGCUUGAUCUAACCAUGU
miR-221/22260671A,m8hsa-miR-221brainAGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brainAGCUACAUCUGGCUACUGGGUCUC
miR-23212521311Ahsa-miR-23abrainAUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrainAUCACAUUGCCAGGGAUUACC
hsa-miR-23abrainAUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrainAUCACAUUGCCAGGGAUUACC
miR-29235523621A,m8hsa-miR-29aSZUAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZUAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZUAGCACCAUUUGAAAUCGGU
miR-320151215181Ahsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA
hsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA
hsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA
miR-329207120781A,m8hsa-miR-329brainAACACACCUGGUUAACCUCUUU
miR-330183318401A,m8hsa-miR-330brainGCAAAGCACACGGCCUGCAGAGA
miR-362232023261Ahsa-miR-362AAUCCUUGGAACCUAGGUGUGAGU
miR-369-3p105710641A,m8hsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
miR-4488418471Ahsa-miR-448UUGCAUAUGUAGGAUGUCCCAU
miR-495883889m8hsa-miR-495brainAAACAAACAUGGUGCACUUCUUU
miR-503101610221Ahsa-miR-503UAGCAGCGGGAACAGUUCUGCAG
miR-505152015261Ahsa-miR-505GUCAACACUUGCUGGUUUCCUC
miR-539125712631Ahsa-miR-539GGAGAAAUUAUCCUUGGUGUGU
miR-93.hd/291-3p/294/295/302/372/373/52022582264m8hsa-miR-93brainAAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302aUAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302bUAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302cUAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302dUAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520eAAAGUGCUUCCUUUUUGAGGG
hsa-miR-520aAAAGUGCUUCCCUUUGGACUGU
hsa-miR-520bAAAGUGCUUCCUUUUAGAGGG
hsa-miR-520cAAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520dAAAGUGCUUCUCUUUGGUGGGUU