Gene Page: PCDHA13
Summary ?
GeneID | 56136 |
Symbol | PCDHA13 |
Synonyms | CNR5|CNRN5|CNRS5|CRNR5|PCDH-ALPHA13 |
Description | protocadherin alpha 13 |
Reference | MIM:606319|HGNC:HGNC:8667|Ensembl:ENSG00000239389|HPRD:07554|Vega:OTTHUMG00000129614 |
Gene type | protein-coding |
Map location | 5q31 |
Pascal p-value | 4.383E-5 |
eGene | Anterior 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 set | Description | Info |
---|---|---|---|
CV:PGCnp | Genome-wide Association Study | GWAS | |
GSMA_I | Genome scan meta-analysis | Psr: 0.0032 |
Section I. Genetics and epigenetics annotation
DNM table
Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
---|---|---|---|---|---|---|---|---|---|---|---|
PCDHA13 | chr5 | 140262375 | C | G | NM_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 | Schizophrenia | DNM:Gulsuner_2013 |
eQTL annotation
SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
---|---|---|---|---|---|---|---|---|
rs251358 | 5 | 140233942 | PCDHA13 | ENSG00000239389.3 | 1.175E-6 | 0 | -27851 | gtex_brain_ba24 |
rs251359 | 5 | 140233976 | PCDHA13 | ENSG00000239389.3 | 1.629E-6 | 0 | -27817 | gtex_brain_ba24 |
rs251360 | 5 | 140234863 | PCDHA13 | ENSG00000239389.3 | 8.768E-9 | 0 | -26930 | gtex_brain_ba24 |
rs251361 | 5 | 140235076 | PCDHA13 | ENSG00000239389.3 | 3.123E-6 | 0 | -26717 | gtex_brain_ba24 |
rs251362 | 5 | 140236950 | PCDHA13 | ENSG00000239389.3 | 2.022E-6 | 0 | -24843 | gtex_brain_ba24 |
rs251363 | 5 | 140237109 | PCDHA13 | ENSG00000239389.3 | 8.523E-9 | 0 | -24684 | gtex_brain_ba24 |
rs251364 | 5 | 140237387 | PCDHA13 | ENSG00000239389.3 | 8.928E-9 | 0 | -24406 | gtex_brain_ba24 |
rs630162 | 5 | 140237548 | PCDHA13 | ENSG00000239389.3 | 8.933E-9 | 0 | -24245 | gtex_brain_ba24 |
rs251365 | 5 | 140239423 | PCDHA13 | ENSG00000239389.3 | 8.428E-9 | 0 | -22370 | gtex_brain_ba24 |
rs251366 | 5 | 140239786 | PCDHA13 | ENSG00000239389.3 | 8.428E-9 | 0 | -22007 | gtex_brain_ba24 |
rs251367 | 5 | 140240426 | PCDHA13 | ENSG00000239389.3 | 2.889E-8 | 0 | -21367 | gtex_brain_ba24 |
rs71574494 | 5 | 140241354 | PCDHA13 | ENSG00000239389.3 | 1.271E-7 | 0 | -20439 | gtex_brain_ba24 |
rs11321479 | 5 | 140242451 | PCDHA13 | ENSG00000239389.3 | 8.428E-9 | 0 | -19342 | gtex_brain_ba24 |
rs251369 | 5 | 140242479 | PCDHA13 | ENSG00000239389.3 | 8.456E-9 | 0 | -19314 | gtex_brain_ba24 |
rs251371 | 5 | 140247354 | PCDHA13 | ENSG00000239389.3 | 8.456E-9 | 0 | -14439 | gtex_brain_ba24 |
rs251374 | 5 | 140252935 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | -8858 | gtex_brain_ba24 |
rs251378 | 5 | 140257591 | PCDHA13 | ENSG00000239389.3 | 8.456E-9 | 0 | -4202 | gtex_brain_ba24 |
rs251379 | 5 | 140258922 | PCDHA13 | ENSG00000239389.3 | 9.861E-9 | 0 | -2871 | gtex_brain_ba24 |
rs59479 | 5 | 140261677 | PCDHA13 | ENSG00000239389.3 | 1.399E-8 | 0 | -116 | gtex_brain_ba24 |
rs251380 | 5 | 140263290 | PCDHA13 | ENSG00000239389.3 | 1.43E-8 | 0 | 1497 | gtex_brain_ba24 |
rs251381 | 5 | 140264855 | PCDHA13 | ENSG00000239389.3 | 1.241E-8 | 0 | 3062 | gtex_brain_ba24 |
rs35160890 | 5 | 140272255 | PCDHA13 | ENSG00000239389.3 | 1.265E-8 | 0 | 10462 | gtex_brain_ba24 |
rs3776121 | 5 | 140274310 | PCDHA13 | ENSG00000239389.3 | 2.1E-7 | 0 | 12517 | gtex_brain_ba24 |
rs13174119 | 5 | 140275674 | PCDHA13 | ENSG00000239389.3 | 9.809E-9 | 0 | 13881 | gtex_brain_ba24 |
rs62384484 | 5 | 140279665 | PCDHA13 | ENSG00000239389.3 | 9.807E-9 | 0 | 17872 | gtex_brain_ba24 |
rs6874218 | 5 | 140280425 | PCDHA13 | ENSG00000239389.3 | 2.612E-8 | 0 | 18632 | gtex_brain_ba24 |
rs34807894 | 5 | 140284031 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 22238 | gtex_brain_ba24 |
rs62384488 | 5 | 140285179 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 23386 | gtex_brain_ba24 |
rs13182228 | 5 | 140285674 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 23881 | gtex_brain_ba24 |
rs7704223 | 5 | 140286119 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 24326 | gtex_brain_ba24 |
rs1606122 | 5 | 140288401 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 26608 | gtex_brain_ba24 |
rs1849054 | 5 | 140288787 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 26994 | gtex_brain_ba24 |
rs1858296 | 5 | 140294163 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 32370 | gtex_brain_ba24 |
rs11167655 | 5 | 140295566 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 33773 | gtex_brain_ba24 |
rs155804 | 5 | 140296749 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 34956 | gtex_brain_ba24 |
rs155803 | 5 | 140296871 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 35078 | gtex_brain_ba24 |
rs155801 | 5 | 140297521 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 35728 | gtex_brain_ba24 |
rs155800 | 5 | 140298378 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 36585 | gtex_brain_ba24 |
rs56003 | 5 | 140298532 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 36739 | gtex_brain_ba24 |
rs56002 | 5 | 140298815 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 37022 | gtex_brain_ba24 |
rs35005979 | 5 | 140299567 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 37774 | gtex_brain_ba24 |
rs155817 | 5 | 140301236 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 39443 | gtex_brain_ba24 |
rs155818 | 5 | 140302162 | PCDHA13 | ENSG00000239389.3 | 8.885E-9 | 0 | 40369 | gtex_brain_ba24 |
rs6149268 | 5 | 140302804 | PCDHA13 | ENSG00000239389.3 | 1.019E-8 | 0 | 41011 | gtex_brain_ba24 |
rs155820 | 5 | 140307746 | PCDHA13 | ENSG00000239389.3 | 9.629E-9 | 0 | 45953 | gtex_brain_ba24 |
rs155821 | 5 | 140309124 | PCDHA13 | ENSG00000239389.3 | 8.768E-8 | 0 | 47331 | gtex_brain_ba24 |
rs397724861 | 5 | 140311045 | PCDHA13 | ENSG00000239389.3 | 8.765E-9 | 0 | 49252 | gtex_brain_ba24 |
rs201955926 | 5 | 140312792 | PCDHA13 | ENSG00000239389.3 | 9.852E-9 | 0 | 50999 | gtex_brain_ba24 |
rs397744827 | 5 | 140312794 | PCDHA13 | ENSG00000239389.3 | 8.908E-9 | 0 | 51001 | gtex_brain_ba24 |
rs155823 | 5 | 140314090 | PCDHA13 | ENSG00000239389.3 | 3.163E-8 | 0 | 52297 | gtex_brain_ba24 |
rs155824 | 5 | 140314280 | PCDHA13 | ENSG00000239389.3 | 8.908E-9 | 0 | 52487 | gtex_brain_ba24 |
rs155825 | 5 | 140315570 | PCDHA13 | ENSG00000239389.3 | 7.938E-9 | 0 | 53777 | gtex_brain_ba24 |
rs246073 | 5 | 140317371 | PCDHA13 | ENSG00000239389.3 | 1.404E-8 | 0 | 55578 | gtex_brain_ba24 |
rs59072362 | 5 | 140318132 | PCDHA13 | ENSG00000239389.3 | 1.002E-8 | 0 | 56339 | gtex_brain_ba24 |
rs199772323 | 5 | 140318137 | PCDHA13 | ENSG00000239389.3 | 1.379E-7 | 0 | 56344 | gtex_brain_ba24 |
rs155816 | 5 | 140320019 | PCDHA13 | ENSG00000239389.3 | 8.924E-9 | 0 | 58226 | gtex_brain_ba24 |
rs155815 | 5 | 140320519 | PCDHA13 | ENSG00000239389.3 | 8.929E-9 | 0 | 58726 | gtex_brain_ba24 |
rs5871754 | 5 | 140320871 | PCDHA13 | ENSG00000239389.3 | 9.179E-9 | 0 | 59078 | gtex_brain_ba24 |
rs246068 | 5 | 140320997 | PCDHA13 | ENSG00000239389.3 | 9.117E-9 | 0 | 59204 | gtex_brain_ba24 |
rs155814 | 5 | 140321593 | PCDHA13 | ENSG00000239389.3 | 8.961E-9 | 0 | 59800 | gtex_brain_ba24 |
rs155813 | 5 | 140323876 | PCDHA13 | ENSG00000239389.3 | 6.06E-9 | 0 | 62083 | gtex_brain_ba24 |
rs269553 | 5 | 140324709 | PCDHA13 | ENSG00000239389.3 | 6.341E-9 | 0 | 62916 | gtex_brain_ba24 |
rs75895301 | 5 | 140326216 | PCDHA13 | ENSG00000239389.3 | 1.292E-6 | 0 | 64423 | gtex_brain_ba24 |
rs246040 | 5 | 140331136 | PCDHA13 | ENSG00000239389.3 | 8.931E-9 | 0 | 69343 | gtex_brain_ba24 |
rs246039 | 5 | 140331337 | PCDHA13 | ENSG00000239389.3 | 1.46E-6 | 0 | 69544 | gtex_brain_ba24 |
rs246015 | 5 | 140335575 | PCDHA13 | ENSG00000239389.3 | 8.162E-9 | 0 | 73782 | gtex_brain_ba24 |
rs155799 | 5 | 140336168 | PCDHA13 | ENSG00000239389.3 | 8.768E-8 | 0 | 74375 | gtex_brain_ba24 |
rs2307694 | 5 | 140336545 | PCDHA13 | ENSG00000239389.3 | 4.264E-8 | 0 | 74752 | gtex_brain_ba24 |
rs5871756 | 5 | 140337437 | PCDHA13 | ENSG00000239389.3 | 8.713E-9 | 0 | 75644 | gtex_brain_ba24 |
rs246004 | 5 | 140340821 | PCDHA13 | ENSG00000239389.3 | 8.976E-9 | 0 | 79028 | gtex_brain_ba24 |
rs151988 | 5 | 140342818 | PCDHA13 | ENSG00000239389.3 | 9.426E-9 | 0 | 81025 | gtex_brain_ba24 |
rs155812 | 5 | 140343372 | PCDHA13 | ENSG00000239389.3 | 9.456E-9 | 0 | 81579 | gtex_brain_ba24 |
rs155811 | 5 | 140343598 | PCDHA13 | ENSG00000239389.3 | 2.213E-8 | 0 | 81805 | gtex_brain_ba24 |
rs155808 | 5 | 140346712 | PCDHA13 | ENSG00000239389.3 | 1.584E-8 | 0 | 84919 | gtex_brain_ba24 |
rs155807 | 5 | 140347053 | PCDHA13 | ENSG00000239389.3 | 1.679E-8 | 0 | 85260 | gtex_brain_ba24 |
rs3776114 | 5 | 140350545 | PCDHA13 | ENSG00000239389.3 | 1.27E-6 | 0 | 88752 | gtex_brain_ba24 |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
PHF20 | 0.97 | 0.97 |
HMG20A | 0.97 | 0.98 |
CSRNP2 | 0.97 | 0.97 |
ZNF512 | 0.96 | 0.96 |
TNPO3 | 0.96 | 0.96 |
POLR3A | 0.96 | 0.98 |
CAPRIN1 | 0.96 | 0.98 |
EXOC2 | 0.96 | 0.97 |
CTTNBP2NL | 0.96 | 0.96 |
STAU1 | 0.96 | 0.97 |
Top 10 negatively co-expressed genes | ||
Gene | Pearson'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 function | GO term | Evidence | Neuro keywords | PubMed ID |
---|---|---|---|---|
GO:0005509 | calcium ion binding | IEA | - | |
GO:0005515 | protein binding | IEA | - | |
Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0007155 | cell adhesion | IEA | - | |
GO:0007156 | homophilic cell adhesion | IEA | - | |
Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
GO:0016021 | integral to membrane | IEA | - | |
GO:0005886 | plasma membrane | IEA | - |
Section V. Pathway annotation
Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
---|---|---|---|
SANSOM APC TARGETS DN | 366 | 238 | All SZGR 2.0 genes in this pathway |
ACEVEDO METHYLATED IN LIVER CANCER DN | 940 | 425 | All SZGR 2.0 genes in this pathway |
MIKKELSEN IPS WITH HCP H3K27ME3 | 102 | 76 | All SZGR 2.0 genes in this pathway |
PEDRIOLI MIR31 TARGETS DN | 418 | 245 | 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-124/506 | 2194 | 2200 | m8 | hsa-miR-506 | UAAGGCACCCUUCUGAGUAGA |
hsa-miR-124brain | UAAGGCACGCGGUGAAUGCC | ||||
miR-15/16/195/424/497 | 1015 | 1022 | 1A,m8 | hsa-miR-15abrain | UAGCAGCACAUAAUGGUUUGUG |
hsa-miR-16brain | UAGCAGCACGUAAAUAUUGGCG | ||||
hsa-miR-15bbrain | UAGCAGCACAUCAUGGUUUACA | ||||
hsa-miR-195SZ | UAGCAGCACAGAAAUAUUGGC | ||||
hsa-miR-424 | CAGCAGCAAUUCAUGUUUUGAA | ||||
hsa-miR-497 | CAGCAGCACACUGUGGUUUGU | ||||
miR-153 | 841 | 847 | 1A | hsa-miR-153 | UUGCAUAGUCACAAAAGUGA |
miR-17-5p/20/93.mr/106/519.d | 2259 | 2265 | m8 | hsa-miR-17-5p | CAAAGUGCUUACAGUGCAGGUAGU |
hsa-miR-20abrain | UAAAGUGCUUAUAGUGCAGGUAG | ||||
hsa-miR-106a | AAAAGUGCUUACAGUGCAGGUAGC | ||||
hsa-miR-106bSZ | UAAAGUGCUGACAGUGCAGAU | ||||
hsa-miR-20bSZ | CAAAGUGCUCAUAGUGCAGGUAG | ||||
hsa-miR-519d | CAAAGUGCCUCCCUUUAGAGUGU | ||||
hsa-miR-17-5p | CAAAGUGCUUACAGUGCAGGUAGU | ||||
hsa-miR-20abrain | UAAAGUGCUUAUAGUGCAGGUAG | ||||
hsa-miR-106a | AAAAGUGCUUACAGUGCAGGUAGC | ||||
hsa-miR-106bSZ | UAAAGUGCUGACAGUGCAGAU | ||||
hsa-miR-20bSZ | CAAAGUGCUCAUAGUGCAGGUAG | ||||
hsa-miR-519d | CAAAGUGCCUCCCUUUAGAGUGU | ||||
miR-181 | 1523 | 1530 | 1A,m8 | hsa-miR-181abrain | AACAUUCAACGCUGUCGGUGAGU |
hsa-miR-181bSZ | AACAUUCAUUGCUGUCGGUGGG | ||||
hsa-miR-181cbrain | AACAUUCAACCUGUCGGUGAGU | ||||
hsa-miR-181dbrain | AACAUUCAUUGUUGUCGGUGGGUU | ||||
miR-185 | 52 | 58 | m8 | hsa-miR-185brain | UGGAGAGAAAGGCAGUUC |
hsa-miR-185brain | UGGAGAGAAAGGCAGUUC | ||||
miR-186 | 791 | 797 | m8 | hsa-miR-186 | CAAAGAAUUCUCCUUUUGGGCUU |
miR-19 | 796 | 803 | 1A,m8 | hsa-miR-19a | UGUGCAAAUCUAUGCAAAACUGA |
hsa-miR-19b | UGUGCAAAUCCAUGCAAAACUGA | ||||
miR-218 | 1791 | 1798 | 1A,m8 | hsa-miR-218brain | UUGUGCUUGAUCUAACCAUGU |
miR-221/222 | 60 | 67 | 1A,m8 | hsa-miR-221brain | AGCUACAUUGUCUGCUGGGUUUC |
hsa-miR-222brain | AGCUACAUCUGGCUACUGGGUCUC | ||||
miR-23 | 2125 | 2131 | 1A | hsa-miR-23abrain | AUCACAUUGCCAGGGAUUUCC |
hsa-miR-23bbrain | AUCACAUUGCCAGGGAUUACC | ||||
hsa-miR-23abrain | AUCACAUUGCCAGGGAUUUCC | ||||
hsa-miR-23bbrain | AUCACAUUGCCAGGGAUUACC | ||||
miR-29 | 2355 | 2362 | 1A,m8 | hsa-miR-29aSZ | UAGCACCAUCUGAAAUCGGUU |
hsa-miR-29bSZ | UAGCACCAUUUGAAAUCAGUGUU | ||||
hsa-miR-29cSZ | UAGCACCAUUUGAAAUCGGU | ||||
miR-320 | 1512 | 1518 | 1A | hsa-miR-320 | AAAAGCUGGGUUGAGAGGGCGAA |
hsa-miR-320 | AAAAGCUGGGUUGAGAGGGCGAA | ||||
hsa-miR-320 | AAAAGCUGGGUUGAGAGGGCGAA | ||||
miR-329 | 2071 | 2078 | 1A,m8 | hsa-miR-329brain | AACACACCUGGUUAACCUCUUU |
miR-330 | 1833 | 1840 | 1A,m8 | hsa-miR-330brain | GCAAAGCACACGGCCUGCAGAGA |
miR-362 | 2320 | 2326 | 1A | hsa-miR-362 | AAUCCUUGGAACCUAGGUGUGAGU |
miR-369-3p | 1057 | 1064 | 1A,m8 | hsa-miR-369-3p | AAUAAUACAUGGUUGAUCUUU |
miR-448 | 841 | 847 | 1A | hsa-miR-448 | UUGCAUAUGUAGGAUGUCCCAU |
miR-495 | 883 | 889 | m8 | hsa-miR-495brain | AAACAAACAUGGUGCACUUCUUU |
miR-503 | 1016 | 1022 | 1A | hsa-miR-503 | UAGCAGCGGGAACAGUUCUGCAG |
miR-505 | 1520 | 1526 | 1A | hsa-miR-505 | GUCAACACUUGCUGGUUUCCUC |
miR-539 | 1257 | 1263 | 1A | hsa-miR-539 | GGAGAAAUUAUCCUUGGUGUGU |
miR-93.hd/291-3p/294/295/302/372/373/520 | 2258 | 2264 | m8 | hsa-miR-93brain | AAAGUGCUGUUCGUGCAGGUAG |
hsa-miR-302a | UAAGUGCUUCCAUGUUUUGGUGA | ||||
hsa-miR-302b | UAAGUGCUUCCAUGUUUUAGUAG | ||||
hsa-miR-302c | UAAGUGCUUCCAUGUUUCAGUGG | ||||
hsa-miR-302d | UAAGUGCUUCCAUGUUUGAGUGU | ||||
hsa-miR-372 | AAAGUGCUGCGACAUUUGAGCGU | ||||
hsa-miR-373 | GAAGUGCUUCGAUUUUGGGGUGU | ||||
hsa-miR-520e | AAAGUGCUUCCUUUUUGAGGG | ||||
hsa-miR-520a | AAAGUGCUUCCCUUUGGACUGU | ||||
hsa-miR-520b | AAAGUGCUUCCUUUUAGAGGG | ||||
hsa-miR-520c | AAAGUGCUUCCUUUUAGAGGGUU | ||||
hsa-miR-520d | AAAGUGCUUCUCUUUGGUGGGUU |
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.