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Center for Computational Systems Medicine
Soverview

Gene summary

Soverview

RNA A-to-I events

Soverview

Differntial gene expression between RNA A-to-I edited versus non-edited samples

Soverview

Protein coding region RNA A-to-I editings

Soverview

The effects of the RNA editing to the miRNA binding sites

Soverview

The effects of the RNA editing to the stability of the RNA structures

Soverview

Relation with ADAR

Soverview

Relation with AD stages

Soverview

Related drugs with this gene

Soverview

Related diseases with this gene


Gene summary for PTCD1

check button Gene summary
Gene informationGene symbol

PTCD1

Gene ID

26024

Gene namepentatricopeptide repeat domain 1
Synonyms-
Cytomap

7q22.1

Type of geneprotein-coding
Descriptionpentatricopeptide repeat-containing protein 1, mitochondrial
Modification date20200313
UniProtAcc

O75127,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PTCD1

GO:0042780

tRNA 3'-end processing

21857155


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RNA A-to-I events for PTCD1

check buttonRNA A-to-I editing events in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure.
* This pie chart shows the number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
all structure

check button RNA editing frequencies across three data sets.
boxplot

check buttonThe number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
boxplot

check button RNA A-to-I editing events in AD.
ADediting_1376918(99431188, -), ADediting_1376919(99431240, -), ADediting_1376920(99431241, -), ADediting_1376921(99431333, -), ADediting_1376922(99431356, -), ADediting_1376923(99431377, -), ADediting_1376924(99431401, -), ADediting_1376925(99431491, -), ADediting_1376926(99431497, -), ADediting_1376927(99431498, -), ADediting_1376928(99431641, -), ADediting_1376929(99431646, -), ADediting_1376930(99431715, -), ADediting_1376931(99436532, -), ADediting_1376932(99459548, -), ADediting_1376933(99459626, -), ADediting_1376934(99461302, -), ADediting_1376935(99461312, -), ADediting_1376936(99461321, -), ADediting_1376937(99461325, -), ADediting_1376938(99461334, -), ADediting_1376939(99461348, -), ADediting_1376940(99461626, -), ADediting_1376941(99461627, -), ADediting_1376942(99461641, -), ADediting_1376943(99461721, -), ADediting_1376944(99461751, -), ADediting_1376945(99461782, -), ADediting_1376946(99461786, -), ADediting_1376947(99461790, -), ADediting_1376948(99461796, -), ADediting_1376949(99461804, -), ADediting_1376950(99461822, -), ADediting_1376951(99461851, -), ADediting_1376952(99461861, -), ADediting_1376953(99461862, -), ADediting_1376954(99461885, -), ADediting_1376955(99461900, -), ADediting_1376956(99461930, -), ADediting_1376957(99461931, -), ADediting_1376958(99462196, -), ADediting_1376959(99462218, -), ADediting_1376960(99462234, -), ADediting_1376961(99462259, -), ADediting_1376962(99462263, -), ADediting_1376963(99462285, -), ADediting_1376964(99462346, -), ADediting_1376965(99462352, -), ADediting_1376966(99462356, -), ADediting_1376967(99462368, -), ADediting_1376968(99462405, -), ADediting_1376969(99462416, -), ADediting_1376970(99462421, -), ADediting_1376971(99462520, -), ADediting_1376972(99462583, -), ADediting_1376973(99462595, -), ADediting_1376974(99462609, -), ADediting_1376975(99462612, -), ADediting_1376976(99462645, -), ADediting_1376977(99462653, -), ADediting_1376978(99462663, -), ADediting_1376979(99462666, -), ADediting_1376980(99462675, -), ADediting_1376981(99462692, -), ADediting_1376982(99462699, -), ADediting_1376983(99462712, -), ADediting_1376984(99462728, -), ADediting_1376985(99462731, -), ADediting_1376986(99462978, -), ADediting_1376987(99463573, -), ADediting_1376988(99463676, -), ADediting_1376989(99463693, -), ADediting_1376990(99463694, -), ADediting_1376991(99463700, -), ADediting_1376992(99463735, -), ADediting_1376993(99464611, -), ADediting_1376994(99465885, -), ADediting_1589240(99461374, -), ADediting_1589241(99461779, -), ADediting_1589242(99463521, -), ADediting_1589243(99463713, -), ADediting_1589244(99463737, -), ADediting_1589245(99464541, -), ADediting_1667626(99461876, -),

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RNA editing positional annotations for PTCD1 using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_1376918chr7_99431188_-intronic
ADediting_1376919chr7_99431240_-intronic
ADediting_1376920chr7_99431241_-intronic
ADediting_1376921chr7_99431333_-intronic
ADediting_1376922chr7_99431356_-intronic
ADediting_1376923chr7_99431377_-intronic
ADediting_1376924chr7_99431401_-intronic
ADediting_1376925chr7_99431491_-intronic
ADediting_1376926chr7_99431497_-intronic
ADediting_1376927chr7_99431498_-intronic
ADediting_1376928chr7_99431641_-intronic
ADediting_1376929chr7_99431646_-intronic
ADediting_1376930chr7_99431715_-intronic
ADediting_1376931chr7_99436532_-intronic
ADediting_1376932chr7_99459548_-intronic
ADediting_1376933chr7_99459626_-intronic
ADediting_1376934chr7_99461302_-intronic
ADediting_1376935chr7_99461312_-intronic
ADediting_1376936chr7_99461321_-intronic
ADediting_1376937chr7_99461325_-intronic
ADediting_1376938chr7_99461334_-intronic
ADediting_1376939chr7_99461348_-intronic
ADediting_1376940chr7_99461626_-intronic
ADediting_1376941chr7_99461627_-intronic
ADediting_1376942chr7_99461641_-intronic
ADediting_1376943chr7_99461721_-intronic
ADediting_1376944chr7_99461751_-intronic
ADediting_1376945chr7_99461782_-intronic
ADediting_1376946chr7_99461786_-intronic
ADediting_1376947chr7_99461790_-intronic
ADediting_1376948chr7_99461796_-intronic
ADediting_1376949chr7_99461804_-intronic
ADediting_1376950chr7_99461822_-intronic
ADediting_1376951chr7_99461851_-intronic
ADediting_1376952chr7_99461861_-intronic
ADediting_1376953chr7_99461862_-intronic
ADediting_1376954chr7_99461885_-intronic
ADediting_1376955chr7_99461900_-intronic
ADediting_1376956chr7_99461930_-intronic
ADediting_1376957chr7_99461931_-intronic
ADediting_1376958chr7_99462196_-intronic
ADediting_1376959chr7_99462218_-intronic
ADediting_1376960chr7_99462234_-intronic
ADediting_1376961chr7_99462259_-intronic
ADediting_1376962chr7_99462263_-intronic
ADediting_1376963chr7_99462285_-intronic
ADediting_1376964chr7_99462346_-intronic
ADediting_1376965chr7_99462352_-intronic
ADediting_1376966chr7_99462356_-intronic
ADediting_1376967chr7_99462368_-intronic
ADediting_1376968chr7_99462405_-intronic
ADediting_1376969chr7_99462416_-intronic
ADediting_1376970chr7_99462421_-intronic
ADediting_1376971chr7_99462520_-intronic
ADediting_1376972chr7_99462583_-intronic
ADediting_1376973chr7_99462595_-intronic
ADediting_1376974chr7_99462609_-intronic
ADediting_1376975chr7_99462612_-intronic
ADediting_1376976chr7_99462645_-intronic
ADediting_1376977chr7_99462653_-intronic
ADediting_1376978chr7_99462663_-intronic
ADediting_1376979chr7_99462666_-intronic
ADediting_1376980chr7_99462675_-intronic
ADediting_1376981chr7_99462692_-intronic
ADediting_1376982chr7_99462699_-intronic
ADediting_1376983chr7_99462712_-intronic
ADediting_1376984chr7_99462728_-intronic
ADediting_1376985chr7_99462731_-intronic
ADediting_1376986chr7_99462978_-intronic
ADediting_1376987chr7_99463573_-intronic
ADediting_1376988chr7_99463676_-intronic
ADediting_1376989chr7_99463693_-intronic
ADediting_1376990chr7_99463694_-intronic
ADediting_1376991chr7_99463700_-intronic
ADediting_1376992chr7_99463735_-intronic
ADediting_1376993chr7_99464611_-intronic
ADediting_1376994chr7_99465885_-intronic
ADediting_1589240chr7_99461374_-intronic
ADediting_1589241chr7_99461779_-intronic
ADediting_1589242chr7_99463521_-intronic
ADediting_1589243chr7_99463713_-intronic
ADediting_1589244chr7_99463737_-intronic
ADediting_1589245chr7_99464541_-intronic
ADediting_1667626chr7_99461876_-intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_1376918chr7_99431188_-SINEAluName=AluSc
ADediting_1376919chr7_99431240_-SINEAluName=AluSc
ADediting_1376920chr7_99431241_-SINEAluName=AluSc
ADediting_1376921chr7_99431333_-SINEAluName=AluSc
ADediting_1376922chr7_99431356_-SINEAluName=AluSc
ADediting_1376923chr7_99431377_-SINEAluName=AluSc
ADediting_1376924chr7_99431401_-SINEAluName=AluSc
ADediting_1376925chr7_99431491_-SINEAluName=AluSz
ADediting_1376926chr7_99431497_-SINEAluName=AluSz
ADediting_1376927chr7_99431498_-SINEAluName=AluSz
ADediting_1376928chr7_99431641_-SINEAluName=AluSz
ADediting_1376929chr7_99431646_-SINEAluName=AluSz
ADediting_1376930chr7_99431715_-SINEAluName=AluSz
ADediting_1376931chr7_99436532_-SINEAluName=AluSx
ADediting_1376932chr7_99459548_-SINEAluName=AluJo
ADediting_1376933chr7_99459626_-SINEAluName=AluJo
ADediting_1376934chr7_99461302_-SINEAluName=FAM
ADediting_1376935chr7_99461312_-SINEAluName=FAM
ADediting_1376936chr7_99461321_-SINEAluName=FAM
ADediting_1376937chr7_99461325_-SINEAluName=FAM
ADediting_1376938chr7_99461334_-SINEAluName=FAM
ADediting_1376939chr7_99461348_-SINEAluName=FAM
ADediting_1376940chr7_99461626_-SINEAluName=AluSz
ADediting_1376941chr7_99461627_-SINEAluName=AluSz
ADediting_1376942chr7_99461641_-SINEAluName=AluSz
ADediting_1376943chr7_99461721_-SINEAluName=AluSx
ADediting_1376944chr7_99461751_-SINEAluName=AluSx
ADediting_1376945chr7_99461782_-SINEAluName=AluSx
ADediting_1376946chr7_99461786_-SINEAluName=AluSx
ADediting_1376947chr7_99461790_-SINEAluName=AluSx
ADediting_1376948chr7_99461796_-SINEAluName=AluSx
ADediting_1376949chr7_99461804_-SINEAluName=AluSx
ADediting_1376950chr7_99461822_-SINEAluName=AluSx
ADediting_1376951chr7_99461851_-SINEAluName=AluSx
ADediting_1376952chr7_99461861_-SINEAluName=AluSx
ADediting_1376953chr7_99461862_-SINEAluName=AluSx
ADediting_1376954chr7_99461885_-SINEAluName=AluSx
ADediting_1376955chr7_99461900_-SINEAluName=AluSx
ADediting_1376956chr7_99461930_-SINEAluName=AluSx
ADediting_1376957chr7_99461931_-SINEAluName=AluSx
ADediting_1376958chr7_99462196_-SINEAluName=AluY
ADediting_1376959chr7_99462218_-SINEAluName=AluY
ADediting_1376960chr7_99462234_-SINEAluName=AluY
ADediting_1376961chr7_99462259_-SINEAluName=AluY
ADediting_1376962chr7_99462263_-SINEAluName=AluY
ADediting_1376963chr7_99462285_-SINEAluName=AluY
ADediting_1376964chr7_99462346_-SINEAluName=AluY
ADediting_1376965chr7_99462352_-SINEAluName=AluY
ADediting_1376966chr7_99462356_-SINEAluName=AluY
ADediting_1376967chr7_99462368_-SINEAluName=AluY
ADediting_1376968chr7_99462405_-SINEAluName=AluY
ADediting_1376969chr7_99462416_-SINEAluName=AluY
ADediting_1376970chr7_99462421_-SINEAluName=AluY
ADediting_1376971chr7_99462520_-SINEAluName=AluSg
ADediting_1376972chr7_99462583_-SINEAluName=AluSg
ADediting_1376973chr7_99462595_-SINEAluName=AluSg
ADediting_1376974chr7_99462609_-SINEAluName=AluSg
ADediting_1376975chr7_99462612_-SINEAluName=AluSg
ADediting_1376976chr7_99462645_-SINEAluName=AluSg
ADediting_1376977chr7_99462653_-SINEAluName=AluSg
ADediting_1376978chr7_99462663_-SINEAluName=AluSg
ADediting_1376979chr7_99462666_-SINEAluName=AluSg
ADediting_1376980chr7_99462675_-SINEAluName=AluSg
ADediting_1376981chr7_99462692_-SINEAluName=AluSg
ADediting_1376982chr7_99462699_-SINEAluName=AluSg
ADediting_1376983chr7_99462712_-SINEAluName=AluSg
ADediting_1376984chr7_99462728_-SINEAluName=AluSg
ADediting_1376985chr7_99462731_-SINEAluName=AluSg
ADediting_1376986chr7_99462978_-SINEMIRName=MIRb
ADediting_1376987chr7_99463573_-SINEAluName=AluSq2
ADediting_1376988chr7_99463676_-SINEAluName=AluSq2
ADediting_1376989chr7_99463693_-SINEAluName=AluSq2
ADediting_1376990chr7_99463694_-SINEAluName=AluSq2
ADediting_1376991chr7_99463700_-SINEAluName=AluSq2
ADediting_1376992chr7_99463735_-SINEAluName=AluSq2
ADediting_1376993chr7_99464611_-SINEAluName=AluYf1
ADediting_1589241chr7_99461779_-SINEAluName=AluSx
ADediting_1589242chr7_99463521_-SINEAluName=AluSq2
ADediting_1589243chr7_99463713_-SINEAluName=AluSq2
ADediting_1589244chr7_99463737_-SINEAluName=AluSq2
ADediting_1589245chr7_99464541_-SINEAluName=AluYf1
ADediting_1667626chr7_99461876_-SINEAluName=AluSx

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RNA A-to-I editing events in the alternative splicing sites for PTCD1

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeADeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength

check button Differential pencent of spliced in (PSI) between RNA A-to-I edited and non-edited samples

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for PTCD1

check button Distribution of the averaged gene expression in AD and control with or without RNA A-to-I editing event.
* The grey color means N/A.

check button Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event.
boxplot
boxplot
boxplot
boxplot

check button - Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.
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check button - Differentially expressed transcript between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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ADeditome IDChrPositoingSkipped exonENSGENSTs

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Protein coding region RNA A-to-I editings for PTCD1

check button- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.


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The effects of the RNA editing to the miRNA binding sites for PTCD1


check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1337757chr7_5495852_-ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-589-3pchr799419634994196418mer-1a9941963499419657149-24.72
ADediting_1337757chr7_5495852_-ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-589-3pchr799419924994199307mer-m89941992399419945144-19.43
ADediting_496066chr15_66496985_-ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-4512chr799418501994185077mer-m89941850099418521152-19.56

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1337757chr7_5495852_-ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-589-3pchr799419159994191657mer-m89941915899419181147-9.41
ADediting_291761chr11_93733708_-ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-1304-3pchr799419367994193748mer-1a9941936799419386152-24.24
ADediting_527135chr16_24203190_+ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-1273h-3pchr799417460994174667mer-m89941745999417481146-16.39
ADediting_843620chr2_207754818_+ENSG00000106246.17ENST00000292478.8PTCD1-201hsa-miR-4775chr799416885994168917mer-m89941688499416905150-6.62

check button Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for PTCD1

check button - RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.
ENSTENST typeRNA structure without RNA A-to-I editing.RNA structure with RNA A-to-I editing.

check button RNA A-to-I editing in miRNA.
ADeditom_IDENSTmir_IDEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in mRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in lncRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

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Relation with ADAR for PTCD1

check button Correlation between ADAR gene expression and RNA editing frequency
TissueADeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)

check button Correlation between ADAR gene expression and this gene's expression
TissueADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
DLPFC5.39305838878757e-320.6023420630746259.8731380797587e-450.6876512629162077.82284574051083e-150.422226936085196
AC2.65210649336541e-420.7265557631731762.196782610046e-290.6328899006827116.35183030993694e-230.569821173140803
PCC4.89257657692178e-260.6679108500048511.79786693612204e-280.691248056936881.5663904241216e-050.306958633521444
CER2.58279979949088e-240.7100980870654991.38064850343653e-320.7850076662888910.0009083081076986490.268137084597986
TCX2.7992196506842e-130.5508639795302772.81900909993662e-060.3717285608212241.53700938221061e-090.468115800873822
FP1.26880222968947e-100.4581802964419259.83465757584438e-190.599270204411860.000351714660343960.264938085132862
IFG0.0004151688026012120.6518365367784050.000261100464537110.668285143408710.009440915783962780.508518770331915
PG0.0004742014337210030.2537630732823222.69514094415814e-050.3025910332618810.4849732093572090.0515170396769925
STG0.0006250750770477590.3656718236611360.004428777159207930.3075561669459340.2789385961099020.11949964435583

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Relation with AD stages for PTCD1

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
TCX0.000189278606350460.354903679965173

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RelatedDrugs for PTCD1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PTCD1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource