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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 NPHP3

check button Gene summary
Gene informationGene symbol

NPHP3

Gene ID

27031

Gene namenephrocystin 3
SynonymsCFAP31|MKS7|NPH3|RHPD|RHPD1|SLSN3
Cytomap

3q22.1

Type of geneprotein-coding
Descriptionnephrocystin-3Meckel syndrome, type 7cilia and flagella associated protein 31nephronophthisis 3 (adolescent)
Modification date20200313
UniProtAcc

Q7Z494,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
NPHP3

GO:0090090

negative regulation of canonical Wnt signaling pathway

18371931


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RNA A-to-I events for NPHP3

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_1023280(132681356, -), ADediting_1023281(132681388, -), ADediting_1023282(132681392, -), ADediting_1023283(132681402, -), ADediting_1023284(132681428, -), ADediting_1023285(132681461, -), ADediting_1023286(132681471, -), ADediting_1023287(132681472, -), ADediting_1023288(132681481, -), ADediting_1023289(132681540, -), ADediting_1023290(132681541, -), ADediting_1023291(132685230, -), ADediting_1023292(132685274, -), ADediting_1023293(132685319, -), ADediting_1023294(132685334, -), ADediting_1023295(132685335, -), ADediting_1023296(132685375, -), ADediting_1023297(132685388, -), ADediting_1023298(132685795, -), ADediting_1023299(132685801, -), ADediting_1023300(132685808, -), ADediting_1023301(132685862, -), ADediting_1023302(132685887, -), ADediting_1023303(132685921, -), ADediting_1023304(132685927, -), ADediting_1023305(132685929, -), ADediting_1023306(132685932, -), ADediting_1023307(132685938, -), ADediting_1023308(132685964, -), ADediting_1023309(132685968, -), ADediting_1023310(132698563, -), ADediting_1023311(132703672, -), ADediting_1023312(132703775, -), ADediting_1023313(132703776, -), ADediting_1023314(132703853, -), ADediting_1023315(132703854, -), ADediting_1023316(132703870, -), ADediting_1023317(132708726, -), ADediting_1023318(132708728, -), ADediting_1023319(132708740, -), ADediting_1023320(132708744, -), ADediting_1023321(132708752, -), ADediting_1023322(132708753, -), ADediting_1023323(132708799, -), ADediting_1023324(132708800, -), ADediting_1023325(132708805, -), ADediting_1023326(132708865, -), ADediting_1023327(132708878, -), ADediting_1023328(132708881, -), ADediting_1023329(132708882, -), ADediting_1023330(132708883, -), ADediting_1023331(132708888, -), ADediting_1023332(132708889, -), ADediting_1023333(132708906, -), ADediting_1023334(132708907, -), ADediting_1023335(132708909, -), ADediting_1023336(132708923, -), ADediting_1023337(132708942, -), ADediting_1023338(132708951, -), ADediting_1023339(132708952, -), ADediting_1023340(132708958, -), ADediting_1023341(132708960, -), ADediting_1023342(132708977, -), ADediting_1023343(132708982, -), ADediting_1023344(132708984, -), ADediting_1023345(132708985, -), ADediting_1023346(132708990, -), ADediting_1023347(132709411, -), ADediting_1023348(132709486, -), ADediting_1023349(132709558, -), ADediting_1023350(132710549, -), ADediting_1023351(132710580, -), ADediting_1023352(132710585, -), ADediting_1023353(132710620, -), ADediting_1023354(132710681, -), ADediting_1023355(132710687, -), ADediting_1023356(132710696, -), ADediting_1023357(132710703, -), ADediting_1023358(132710755, -), ADediting_1023359(132710756, -), ADediting_1023360(132710764, -), ADediting_1023361(132710765, -), ADediting_1023362(132710800, -), ADediting_1023363(132710869, -), ADediting_1023364(132710879, -), ADediting_1023365(132710880, -), ADediting_1023366(132712577, -), ADediting_1023367(132717825, -), ADediting_1023368(132717826, -), ADediting_1572138(132685252, -), ADediting_1572139(132685258, -), ADediting_1572140(132685260, -), ADediting_1572141(132685270, -), ADediting_1572142(132685339, -), ADediting_1572143(132685383, -), ADediting_1572144(132685389, -), ADediting_1572145(132685397, -), ADediting_1572146(132685402, -), ADediting_1572147(132686045, -), ADediting_1572148(132703783, -), ADediting_1572149(132703876, -), ADediting_1572150(132717896, -), ADediting_1644362(132685951, -), ADediting_1644363(132708902, -), ADediting_1644364(132709447, -),

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RNA editing positional annotations for NPHP3 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_1023280chr3_132681356_-UTR3
ADediting_1023281chr3_132681388_-UTR3
ADediting_1023282chr3_132681392_-UTR3
ADediting_1023283chr3_132681402_-UTR3
ADediting_1023284chr3_132681428_-UTR3
ADediting_1023285chr3_132681461_-UTR3
ADediting_1023286chr3_132681471_-UTR3
ADediting_1023287chr3_132681472_-UTR3
ADediting_1023288chr3_132681481_-UTR3
ADediting_1023289chr3_132681540_-UTR3
ADediting_1023290chr3_132681541_-UTR3
ADediting_1023291chr3_132685230_-intronic
ADediting_1023292chr3_132685274_-intronic
ADediting_1023293chr3_132685319_-intronic
ADediting_1023294chr3_132685334_-intronic
ADediting_1023295chr3_132685335_-intronic
ADediting_1023296chr3_132685375_-intronic
ADediting_1023297chr3_132685388_-intronic
ADediting_1023298chr3_132685795_-intronic
ADediting_1023299chr3_132685801_-intronic
ADediting_1023300chr3_132685808_-intronic
ADediting_1023301chr3_132685862_-intronic
ADediting_1023302chr3_132685887_-intronic
ADediting_1023303chr3_132685921_-intronic
ADediting_1023304chr3_132685927_-intronic
ADediting_1023305chr3_132685929_-intronic
ADediting_1023306chr3_132685932_-intronic
ADediting_1023307chr3_132685938_-intronic
ADediting_1023308chr3_132685964_-intronic
ADediting_1023309chr3_132685968_-intronic
ADediting_1023310chr3_132698563_-intronic
ADediting_1023311chr3_132703672_-intronic
ADediting_1023312chr3_132703775_-intronic
ADediting_1023313chr3_132703776_-intronic
ADediting_1023314chr3_132703853_-intronic
ADediting_1023315chr3_132703854_-intronic
ADediting_1023316chr3_132703870_-intronic
ADediting_1023317chr3_132708726_-intronic
ADediting_1023318chr3_132708728_-intronic
ADediting_1023319chr3_132708740_-intronic
ADediting_1023320chr3_132708744_-intronic
ADediting_1023321chr3_132708752_-intronic
ADediting_1023322chr3_132708753_-intronic
ADediting_1023323chr3_132708799_-intronic
ADediting_1023324chr3_132708800_-intronic
ADediting_1023325chr3_132708805_-intronic
ADediting_1023326chr3_132708865_-intronic
ADediting_1023327chr3_132708878_-intronic
ADediting_1023328chr3_132708881_-intronic
ADediting_1023329chr3_132708882_-intronic
ADediting_1023330chr3_132708883_-intronic
ADediting_1023331chr3_132708888_-intronic
ADediting_1023332chr3_132708889_-intronic
ADediting_1023333chr3_132708906_-intronic
ADediting_1023334chr3_132708907_-intronic
ADediting_1023335chr3_132708909_-intronic
ADediting_1023336chr3_132708923_-intronic
ADediting_1023337chr3_132708942_-intronic
ADediting_1023338chr3_132708951_-intronic
ADediting_1023339chr3_132708952_-intronic
ADediting_1023340chr3_132708958_-intronic
ADediting_1023341chr3_132708960_-intronic
ADediting_1023342chr3_132708977_-intronic
ADediting_1023343chr3_132708982_-intronic
ADediting_1023344chr3_132708984_-intronic
ADediting_1023345chr3_132708985_-intronic
ADediting_1023346chr3_132708990_-intronic
ADediting_1023347chr3_132709411_-intronic
ADediting_1023348chr3_132709486_-intronic
ADediting_1023349chr3_132709558_-intronic
ADediting_1023350chr3_132710549_-intronic
ADediting_1023351chr3_132710580_-intronic
ADediting_1023352chr3_132710585_-intronic
ADediting_1023353chr3_132710620_-intronic
ADediting_1023354chr3_132710681_-intronic
ADediting_1023355chr3_132710687_-intronic
ADediting_1023356chr3_132710696_-intronic
ADediting_1023357chr3_132710703_-intronic
ADediting_1023358chr3_132710755_-intronic
ADediting_1023359chr3_132710756_-intronic
ADediting_1023360chr3_132710764_-intronic
ADediting_1023361chr3_132710765_-intronic
ADediting_1023362chr3_132710800_-intronic
ADediting_1023363chr3_132710869_-intronic
ADediting_1023364chr3_132710879_-intronic
ADediting_1023365chr3_132710880_-intronic
ADediting_1023366chr3_132712577_-intronic
ADediting_1023367chr3_132717825_-intronic
ADediting_1023368chr3_132717826_-intronic
ADediting_1572138chr3_132685252_-intronic
ADediting_1572139chr3_132685258_-intronic
ADediting_1572140chr3_132685260_-intronic
ADediting_1572141chr3_132685270_-intronic
ADediting_1572142chr3_132685339_-intronic
ADediting_1572143chr3_132685383_-intronic
ADediting_1572144chr3_132685389_-intronic
ADediting_1572145chr3_132685397_-intronic
ADediting_1572146chr3_132685402_-intronic
ADediting_1572147chr3_132686045_-intronic
ADediting_1572148chr3_132703783_-intronic
ADediting_1572149chr3_132703876_-intronic
ADediting_1572150chr3_132717896_-intronic
ADediting_1644362chr3_132685951_-intronic
ADediting_1644363chr3_132708902_-intronic
ADediting_1644364chr3_132709447_-intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_1023280chr3_132681356_-SINEAluName=AluSz6
ADediting_1023281chr3_132681388_-SINEAluName=AluSz6
ADediting_1023282chr3_132681392_-SINEAluName=AluSz6
ADediting_1023283chr3_132681402_-SINEAluName=AluSz6
ADediting_1023284chr3_132681428_-SINEAluName=AluSz6
ADediting_1023285chr3_132681461_-SINEAluName=AluSz6
ADediting_1023286chr3_132681471_-SINEAluName=AluSz6
ADediting_1023287chr3_132681472_-SINEAluName=AluSz6
ADediting_1023288chr3_132681481_-SINEAluName=AluSz6
ADediting_1023289chr3_132681540_-SINEAluName=AluSz6
ADediting_1023290chr3_132681541_-SINEAluName=AluSz6
ADediting_1023291chr3_132685230_-SINEAluName=AluJr
ADediting_1023292chr3_132685274_-SINEAluName=AluJr
ADediting_1023293chr3_132685319_-SINEAluName=AluJr
ADediting_1023294chr3_132685334_-SINEAluName=AluJr
ADediting_1023295chr3_132685335_-SINEAluName=AluJr
ADediting_1023296chr3_132685375_-SINEAluName=AluJr
ADediting_1023297chr3_132685388_-SINEAluName=AluJr
ADediting_1023298chr3_132685795_-SINEAluName=AluSc8
ADediting_1023299chr3_132685801_-SINEAluName=AluSc8
ADediting_1023300chr3_132685808_-SINEAluName=AluSc8
ADediting_1023301chr3_132685862_-SINEAluName=AluSc8
ADediting_1023302chr3_132685887_-SINEAluName=AluSc8
ADediting_1023303chr3_132685921_-SINEAluName=AluSc8
ADediting_1023304chr3_132685927_-SINEAluName=AluSc8
ADediting_1023305chr3_132685929_-SINEAluName=AluSc8
ADediting_1023306chr3_132685932_-SINEAluName=AluSc8
ADediting_1023307chr3_132685938_-SINEAluName=AluSc8
ADediting_1023308chr3_132685964_-SINEAluName=AluSc8
ADediting_1023309chr3_132685968_-SINEAluName=AluSc8
ADediting_1023310chr3_132698563_-SINEAluName=AluSq2
ADediting_1023311chr3_132703672_-SINEAluName=AluJb
ADediting_1023312chr3_132703775_-SINEAluName=AluJb
ADediting_1023313chr3_132703776_-SINEAluName=AluJb
ADediting_1023314chr3_132703853_-SINEAluName=AluJb
ADediting_1023315chr3_132703854_-SINEAluName=AluJb
ADediting_1023316chr3_132703870_-SINEAluName=AluJb
ADediting_1023317chr3_132708726_-LINERTE-XName=L4_A_Mam
ADediting_1023318chr3_132708728_-LINERTE-XName=L4_A_Mam
ADediting_1023319chr3_132708740_-LINERTE-XName=L4_A_Mam
ADediting_1023320chr3_132708744_-LINERTE-XName=L4_A_Mam
ADediting_1023321chr3_132708752_-LINERTE-XName=L4_A_Mam
ADediting_1023322chr3_132708753_-LINERTE-XName=L4_A_Mam
ADediting_1023323chr3_132708799_-LINERTE-XName=L4_A_Mam
ADediting_1023324chr3_132708800_-LINERTE-XName=L4_A_Mam
ADediting_1023325chr3_132708805_-LINERTE-XName=L4_A_Mam
ADediting_1023326chr3_132708865_-LINERTE-XName=L4_A_Mam
ADediting_1023327chr3_132708878_-LINERTE-XName=L4_A_Mam
ADediting_1023328chr3_132708881_-LINERTE-XName=L4_A_Mam
ADediting_1023329chr3_132708882_-LINERTE-XName=L4_A_Mam
ADediting_1023330chr3_132708883_-LINERTE-XName=L4_A_Mam
ADediting_1023331chr3_132708888_-LINERTE-XName=L4_A_Mam
ADediting_1023332chr3_132708889_-LINERTE-XName=L4_A_Mam
ADediting_1023333chr3_132708906_-LINERTE-XName=L4_A_Mam
ADediting_1023334chr3_132708907_-LINERTE-XName=L4_A_Mam
ADediting_1023335chr3_132708909_-LINERTE-XName=L4_A_Mam
ADediting_1023336chr3_132708923_-LINERTE-XName=L4_A_Mam
ADediting_1023337chr3_132708942_-LINERTE-XName=L4_A_Mam
ADediting_1023338chr3_132708951_-LINERTE-XName=L4_A_Mam
ADediting_1023339chr3_132708952_-LINERTE-XName=L4_A_Mam
ADediting_1023340chr3_132708958_-LINERTE-XName=L4_A_Mam
ADediting_1023341chr3_132708960_-LINERTE-XName=L4_A_Mam
ADediting_1023347chr3_132709411_-SINEAluName=AluJb
ADediting_1023348chr3_132709486_-SINEAluName=AluJb
ADediting_1023349chr3_132709558_-SINEAluName=AluJb
ADediting_1023350chr3_132710549_-LINERTE-XName=L4_A_Mam
ADediting_1023351chr3_132710580_-LINERTE-XName=L4_A_Mam
ADediting_1023352chr3_132710585_-LINERTE-XName=L4_A_Mam
ADediting_1023353chr3_132710620_-LINERTE-XName=L4_A_Mam
ADediting_1023354chr3_132710681_-LINERTE-XName=L4_A_Mam
ADediting_1023355chr3_132710687_-LINERTE-XName=L4_A_Mam
ADediting_1023356chr3_132710696_-LINERTE-XName=L4_A_Mam
ADediting_1023357chr3_132710703_-LINERTE-XName=L4_A_Mam
ADediting_1023358chr3_132710755_-LINERTE-XName=L4_A_Mam
ADediting_1023359chr3_132710756_-LINERTE-XName=L4_A_Mam
ADediting_1023360chr3_132710764_-LINERTE-XName=L4_A_Mam
ADediting_1023361chr3_132710765_-LINERTE-XName=L4_A_Mam
ADediting_1023362chr3_132710800_-LINERTE-XName=L4_A_Mam
ADediting_1023363chr3_132710869_-LINERTE-XName=L4_A_Mam
ADediting_1023364chr3_132710879_-LINERTE-XName=L4_A_Mam
ADediting_1023365chr3_132710880_-LINERTE-XName=L4_A_Mam
ADediting_1023366chr3_132712577_-SINEAluName=AluY
ADediting_1023367chr3_132717825_-SINEAluName=AluSc
ADediting_1023368chr3_132717826_-SINEAluName=AluSc
ADediting_1572138chr3_132685252_-SINEAluName=AluJr
ADediting_1572139chr3_132685258_-SINEAluName=AluJr
ADediting_1572140chr3_132685260_-SINEAluName=AluJr
ADediting_1572141chr3_132685270_-SINEAluName=AluJr
ADediting_1572142chr3_132685339_-SINEAluName=AluJr
ADediting_1572143chr3_132685383_-SINEAluName=AluJr
ADediting_1572144chr3_132685389_-SINEAluName=AluJr
ADediting_1572145chr3_132685397_-SINEAluName=AluJr
ADediting_1572146chr3_132685402_-SINEAluName=AluJr
ADediting_1572147chr3_132686045_-SINEAluName=AluSc8
ADediting_1572148chr3_132703783_-SINEAluName=AluJb
ADediting_1572149chr3_132703876_-SINEAluName=AluJb
ADediting_1572150chr3_132717896_-SINEAluName=AluSc
ADediting_1644362chr3_132685951_-SINEAluName=AluSc8
ADediting_1644363chr3_132708902_-LINERTE-XName=L4_A_Mam
ADediting_1644364chr3_132709447_-SINEAluName=AluJb

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RNA A-to-I editing events in the alternative splicing sites for NPHP3

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 NPHP3

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
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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.

Soverview
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ADeditome IDChrPositoingSkipped exonENSGENSTs