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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 TTC38

check button Gene summary
Gene informationGene symbol

TTC38

Gene ID

55020

Gene nametetratricopeptide repeat domain 38
SynonymsLL22NC03-5H6.5
Cytomap

22q13.31

Type of geneprotein-coding
Descriptiontetratricopeptide repeat protein 38TPR repeat protein 38
Modification date20200313
UniProtAcc

Q5R3I4,

Context

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

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RNA A-to-I events for TTC38

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_1004578(46269873, +), ADediting_1004579(46269977, +), ADediting_1004580(46270054, +), ADediting_1004581(46270631, +), ADediting_1004582(46270647, +), ADediting_1004583(46270668, +), ADediting_1004584(46270671, +), ADediting_1004585(46270672, +), ADediting_1004586(46270688, +), ADediting_1004587(46270714, +), ADediting_1004588(46270715, +), ADediting_1004589(46270788, +), ADediting_1004590(46270821, +), ADediting_1004591(46270875, +), ADediting_1004592(46270882, +), ADediting_1004593(46270944, +), ADediting_1004594(46270962, +), ADediting_1004595(46271272, +), ADediting_1004596(46271352, +), ADediting_1004597(46271394, +), ADediting_1004598(46271397, +), ADediting_1004599(46271420, +), ADediting_1004600(46271474, +), ADediting_1004601(46271475, +), ADediting_1004602(46271565, +), ADediting_1004603(46271582, +), ADediting_1004604(46271644, +), ADediting_1004605(46271694, +), ADediting_1004606(46272055, +), ADediting_1004607(46272056, +), ADediting_1004608(46272077, +), ADediting_1004609(46272174, +), ADediting_1004610(46282953, +), ADediting_1004611(46283732, +), ADediting_1004612(46283745, +), ADediting_1004613(46283758, +), ADediting_1004614(46283773, +), ADediting_1004615(46291835, +), ADediting_1004616(46292208, +), ADediting_1004617(46292235, +), ADediting_1004618(46292253, +), ADediting_1004619(46292284, +), ADediting_1004620(46292287, +), ADediting_1571352(46270754, +), ADediting_1571353(46291862, +), ADediting_1571354(46291877, +), ADediting_1571355(46291906, +), ADediting_1571356(46292251, +), ADediting_1571357(46292270, +), ADediting_1642991(46270657, +),

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RNA editing positional annotations for TTC38 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_1004578chr22_46269873_+intronic
ADediting_1004579chr22_46269977_+intronic
ADediting_1004580chr22_46270054_+intronic
ADediting_1004581chr22_46270631_+intronic
ADediting_1004582chr22_46270647_+intronic
ADediting_1004583chr22_46270668_+intronic
ADediting_1004584chr22_46270671_+intronic
ADediting_1004585chr22_46270672_+intronic
ADediting_1004586chr22_46270688_+intronic
ADediting_1004587chr22_46270714_+intronic
ADediting_1004588chr22_46270715_+intronic
ADediting_1004589chr22_46270788_+intronic
ADediting_1004590chr22_46270821_+intronic
ADediting_1004591chr22_46270875_+intronic
ADediting_1004592chr22_46270882_+intronic
ADediting_1004593chr22_46270944_+intronic
ADediting_1004594chr22_46270962_+intronic
ADediting_1004595chr22_46271272_+intronic
ADediting_1004596chr22_46271352_+intronic
ADediting_1004597chr22_46271394_+intronic
ADediting_1004598chr22_46271397_+intronic
ADediting_1004599chr22_46271420_+intronic
ADediting_1004600chr22_46271474_+intronic
ADediting_1004601chr22_46271475_+intronic
ADediting_1004602chr22_46271565_+intronic
ADediting_1004603chr22_46271582_+intronic
ADediting_1004604chr22_46271644_+intronic
ADediting_1004605chr22_46271694_+intronic
ADediting_1004606chr22_46272055_+intronic
ADediting_1004607chr22_46272056_+intronic
ADediting_1004608chr22_46272077_+intronic
ADediting_1004609chr22_46272174_+intronic
ADediting_1004610chr22_46282953_+intronic
ADediting_1004611chr22_46283732_+intronic
ADediting_1004612chr22_46283745_+intronic
ADediting_1004613chr22_46283758_+intronic
ADediting_1004614chr22_46283773_+intronic
ADediting_1004615chr22_46291835_+intronic
ADediting_1004616chr22_46292208_+exonic
ADediting_1004617chr22_46292235_+exonic
ADediting_1004618chr22_46292253_+UTR3
ADediting_1004619chr22_46292284_+UTR3
ADediting_1004620chr22_46292287_+UTR3
ADediting_1571352chr22_46270754_+intronic
ADediting_1571353chr22_46291862_+intronic
ADediting_1571354chr22_46291877_+intronic
ADediting_1571355chr22_46291906_+intronic
ADediting_1571356chr22_46292251_+UTR3
ADediting_1571357chr22_46292270_+UTR3
ADediting_1642991chr22_46270657_+intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_1004578chr22_46269873_+SINEAluName=AluSx3
ADediting_1004579chr22_46269977_+SINEAluName=AluSx3
ADediting_1004580chr22_46270054_+SINEAluName=AluSx3
ADediting_1004581chr22_46270631_+SINEAluName=AluSx
ADediting_1004582chr22_46270647_+SINEAluName=AluSx
ADediting_1004583chr22_46270668_+SINEAluName=AluSx
ADediting_1004584chr22_46270671_+SINEAluName=AluSx
ADediting_1004585chr22_46270672_+SINEAluName=AluSx
ADediting_1004586chr22_46270688_+SINEAluName=AluSx
ADediting_1004587chr22_46270714_+SINEAluName=AluSx
ADediting_1004588chr22_46270715_+SINEAluName=AluSx
ADediting_1004589chr22_46270788_+SINEAluName=AluSx
ADediting_1004590chr22_46270821_+SINEAluName=AluSx
ADediting_1004591chr22_46270875_+SINEAluName=AluSx
ADediting_1004592chr22_46270882_+SINEAluName=AluSx
ADediting_1004593chr22_46270944_+SINEAluName=AluSx
ADediting_1004594chr22_46270962_+SINEAluName=AluSx
ADediting_1004595chr22_46271272_+SINEAluName=AluY
ADediting_1004596chr22_46271352_+SINEAluName=AluY
ADediting_1004597chr22_46271394_+SINEAluName=AluY
ADediting_1004598chr22_46271397_+SINEAluName=AluY
ADediting_1004599chr22_46271420_+SINEAluName=AluY
ADediting_1004600chr22_46271474_+SINEAluName=AluY
ADediting_1004601chr22_46271475_+SINEAluName=AluY
ADediting_1004602chr22_46271565_+SINEAluName=AluSz6
ADediting_1004603chr22_46271582_+SINEAluName=AluSz6
ADediting_1004604chr22_46271644_+SINEAluName=AluSz6
ADediting_1004605chr22_46271694_+SINEAluName=AluSz6
ADediting_1004606chr22_46272055_+SINEAluName=AluSx
ADediting_1004607chr22_46272056_+SINEAluName=AluSx
ADediting_1004608chr22_46272077_+SINEAluName=AluSx
ADediting_1004609chr22_46272174_+SINEAluName=AluSx
ADediting_1004610chr22_46282953_+SINEAluName=AluJb
ADediting_1004611chr22_46283732_+SINEAluName=AluSx
ADediting_1004612chr22_46283745_+SINEAluName=AluSx
ADediting_1004613chr22_46283758_+SINEAluName=AluSx
ADediting_1004614chr22_46283773_+SINEAluName=AluSx
ADediting_1004615chr22_46291835_+SINEAluName=AluSx1
ADediting_1004616chr22_46292208_+SINEAluName=AluJr4
ADediting_1004617chr22_46292235_+SINEAluName=AluJr4
ADediting_1004618chr22_46292253_+SINEAluName=AluJr4
ADediting_1004619chr22_46292284_+SINEAluName=AluJr4
ADediting_1004620chr22_46292287_+SINEAluName=AluJr4
ADediting_1571352chr22_46270754_+SINEAluName=AluSx
ADediting_1571353chr22_46291862_+SINEAluName=AluSx1
ADediting_1571354chr22_46291877_+SINEAluName=AluSx1
ADediting_1571355chr22_46291906_+SINEAluName=AluSx1
ADediting_1571356chr22_46292251_+SINEAluName=AluJr4
ADediting_1571357chr22_46292270_+SINEAluName=AluJr4
ADediting_1642991chr22_46270657_+SINEAluName=AluSx

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RNA A-to-I editing events in the alternative splicing sites for TTC38

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 TTC38

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

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.
Soverview

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.

Soverview
Soverview
Soverview
ADeditome IDChrPositoingSkipped exonENSGENSTs

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Protein coding region RNA A-to-I editings for TTC38

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 TTC38


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_-ENSG00000075234.17ENST00000381031.8TTC38-201hsa-miR-589-3pchr2246293667462936737mer-m84629365146293674147-16.87
ADediting_1535951chr14_100874558_+ENSG00000075234.17ENST00000381031.8TTC38-201hsa-miR-337-3pchr2246293018462930258mer-1a4629300446293025144-10.42
ADediting_496066chr15_66496985_-ENSG00000075234.17ENST00000381031.8TTC38-201hsa-miR-4512chr2246293421462934277mer-m84629340546293428154-24.06

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_1097295chr3_85385762_+ENSG00000075234.17ENST00000381031.8TTC38-201hsa-miR-5688chr2246292983462929908mer-1a4629296946292990145-13.77

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 TTC38

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 TTC38

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.)
CERADediting_1004617chr22_46292235_+0.0001923227681441930.2999317961673575.21447974505174e-090.4543532149907990.000985237175177070.266363133438214
TCXADediting_1004617chr22_46292235_+0.7441561217239040.02686667821108740.119929847552765-0.1275186065542050.0001155379093690010.309611790573282
CERADediting_1004618chr22_46292253_+2.77143431384853e-080.4344878415472856.23213163186108e-170.6143267051710790.006708154875623790.22046575220738
CERADediting_1571356chr22_46292251_+0.001794555373826440.2528916424102773.63834589485278e-070.4011273966376560.1197876178273250.127567204813295

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.)
DLPFC0.004824599969941450.159697545156580.1111562926884490.09065714053963919.6737240285654e-190.473656863960034
AC9.92769469866926e-260.5989413870941741.41793109299952e-110.4103777174046629.55291619031965e-300.636033384644775
CER1.73328596864147e-100.491280374633072.10913742048447e-120.5333656988032578.3837606783701e-110.498621035676808
TCX0.03935691563872530.1684389632134020.0101393719029498-0.2093443655847234.82012105603461e-190.645455450155261
FP0.0002492083054279050.2713026348444350.1386882274305630.1114218027565631.34851260491148e-150.552200245732791
IFG0.4004360880082640.1758553447694910.3273944271317090.2042569266775990.0007736870250349970.628131351130836
PG0.725441736789046-0.02592131396711420.410996366993431-0.0606356095200898.32347933304011e-150.529046667678043
STG0.07936196757184820.1925104243077190.39010459503236-0.09498220267595693.46871346423724e-090.590148899296313

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Relation with AD stages for TTC38

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.
CERADediting_1004617chr22_46292235_+0.0005729483999857660.326096347019962
CERADediting_1004618chr22_46292253_+6.35423826334108e-060.419089851353372
CERADediting_1571356chr22_46292251_+0.001457046665084740.302601232389766

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
CER5.2152746343519e-070.460789080637548
TCX3.74261764621961e-070.469876331359243

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RelatedDrugs for TTC38

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 TTC38

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