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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 USP31

check button Gene summary
Gene informationGene symbol

USP31

Gene ID

57478

Gene nameubiquitin specific peptidase 31
Synonyms-
Cytomap

16p12.2

Type of geneprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase 31deubiquitinating enzyme 31ubiquitin specific proteinase 31ubiquitin thioesterase 31ubiquitin thiolesterase 31ubiquitin-specific-processing protease 31
Modification date20200313
UniProtAcc

Q70CQ4,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
USP31

GO:0016579

protein deubiquitination

16214042


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RNA A-to-I events for USP31

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_524367(23068470, -), ADediting_524471(23117927, -), ADediting_524472(23118020, -), ADediting_524473(23118062, -), ADediting_524474(23118068, -), ADediting_524475(23118833, -), ADediting_524476(23118851, -), ADediting_524477(23118890, -), ADediting_524478(23118891, -), ADediting_524479(23118910, -), ADediting_524480(23118911, -), ADediting_524481(23119164, -), ADediting_524482(23119166, -), ADediting_524483(23119171, -), ADediting_524484(23119195, -), ADediting_524485(23119196, -), ADediting_524486(23119236, -), ADediting_524487(23119373, -), ADediting_524488(23119389, -), ADediting_524496(23127236, -), ADediting_524498(23127305, -), ADediting_524499(23127315, -), ADediting_524500(23127344, -), ADediting_524501(23127351, -), ADediting_524502(23127356, -), ADediting_524503(23127362, -), ADediting_524504(23127517, -), ADediting_524505(23127555, -), ADediting_524506(23127750, -), ADediting_524524(23133929, -), ADediting_524525(23133947, -), ADediting_524526(23133994, -), ADediting_524527(23134063, -), ADediting_524541(23139319, -), ADediting_524542(23141470, -), ADediting_524543(23141485, -), ADediting_524544(23141506, -), ADediting_524545(23141571, -), ADediting_524546(23141578, -), ADediting_524547(23141595, -), ADediting_524548(23141596, -), ADediting_524549(23141649, -), ADediting_524550(23141650, -), ADediting_524551(23144527, -), ADediting_524552(23144572, -), ADediting_524553(23144576, -), ADediting_524554(23144617, -), ADediting_524555(23144754, -), ADediting_524556(23144755, -), ADediting_524558(23146416, -), ADediting_524559(23146437, -), ADediting_524560(23146481, -), ADediting_524565(23147134, -), ADediting_524566(23147144, -), ADediting_524567(23147181, -), ADediting_524568(23147205, -), ADediting_524569(23147220, -), ADediting_524570(23147233, -), ADediting_524571(23147237, -), ADediting_524572(23147246, -), ADediting_524573(23147255, -), ADediting_524574(23147341, -), ADediting_524575(23147381, -), ADediting_524576(23147382, -), ADediting_524577(23147682, -), ADediting_524578(23147710, -), ADediting_524579(23147711, -), ADediting_524580(23147736, -), ADediting_524581(23147815, -), ADediting_524582(23147861, -), ADediting_524583(23147862, -), ADediting_524585(23147931, -), ADediting_1541439(23147311, -), ADediting_1624068(23126211, -), ADediting_1624069(23127184, -), ADediting_1624070(23127283, -), ADediting_1624071(23127327, -), ADediting_1624072(23127410, -), ADediting_1624073(23147284, -), ADediting_1624074(23147937, -), ADediting_1624075(23147942, -), ADediting_1624076(23147948, -),

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RNA editing positional annotations for USP31 using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred
ADediting_524367chr16_23068470_-nonsynonymous SNVENST00000219689.11c.A3635Gp.K1212R1.00.00.16
ADediting_524367chr16_23068470_-nonsynonymous SNVENST00000567975.1c.A1514Gp.K505R1.00.00.16

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_524367chr16_23068470_-exonic
ADediting_524471chr16_23117927_-intronic
ADediting_524472chr16_23118020_-intronic
ADediting_524473chr16_23118062_-intronic
ADediting_524474chr16_23118068_-intronic
ADediting_524475chr16_23118833_-intronic
ADediting_524476chr16_23118851_-intronic
ADediting_524477chr16_23118890_-intronic
ADediting_524478chr16_23118891_-intronic
ADediting_524479chr16_23118910_-intronic
ADediting_524480chr16_23118911_-intronic
ADediting_524481chr16_23119164_-intronic
ADediting_524482chr16_23119166_-intronic
ADediting_524483chr16_23119171_-intronic
ADediting_524484chr16_23119195_-intronic
ADediting_524485chr16_23119196_-intronic
ADediting_524486chr16_23119236_-intronic
ADediting_524487chr16_23119373_-intronic
ADediting_524488chr16_23119389_-intronic
ADediting_524496chr16_23127236_-intronic
ADediting_524498chr16_23127305_-intronic
ADediting_524499chr16_23127315_-intronic
ADediting_524500chr16_23127344_-intronic
ADediting_524501chr16_23127351_-intronic
ADediting_524502chr16_23127356_-intronic
ADediting_524503chr16_23127362_-intronic
ADediting_524504chr16_23127517_-intronic
ADediting_524505chr16_23127555_-intronic
ADediting_524506chr16_23127750_-intronic
ADediting_524524chr16_23133929_-intronic
ADediting_524525chr16_23133947_-intronic
ADediting_524526chr16_23133994_-intronic
ADediting_524527chr16_23134063_-intronic
ADediting_524541chr16_23139319_-intronic
ADediting_524542chr16_23141470_-intronic
ADediting_524543chr16_23141485_-intronic
ADediting_524544chr16_23141506_-intronic
ADediting_524545chr16_23141571_-intronic
ADediting_524546chr16_23141578_-intronic
ADediting_524547chr16_23141595_-intronic
ADediting_524548chr16_23141596_-intronic
ADediting_524549chr16_23141649_-intronic
ADediting_524550chr16_23141650_-intronic
ADediting_524551chr16_23144527_-intronic
ADediting_524552chr16_23144572_-intronic
ADediting_524553chr16_23144576_-intronic
ADediting_524554chr16_23144617_-intronic
ADediting_524555chr16_23144754_-intronic
ADediting_524556chr16_23144755_-intronic
ADediting_524558chr16_23146416_-intronic
ADediting_524559chr16_23146437_-intronic
ADediting_524560chr16_23146481_-intronic
ADediting_524565chr16_23147134_-intronic
ADediting_524566chr16_23147144_-intronic
ADediting_524567chr16_23147181_-intronic
ADediting_524568chr16_23147205_-intronic
ADediting_524569chr16_23147220_-intronic
ADediting_524570chr16_23147233_-intronic
ADediting_524571chr16_23147237_-intronic
ADediting_524572chr16_23147246_-intronic
ADediting_524573chr16_23147255_-intronic
ADediting_524574chr16_23147341_-intronic
ADediting_524575chr16_23147381_-intronic
ADediting_524576chr16_23147382_-intronic
ADediting_524577chr16_23147682_-intronic
ADediting_524578chr16_23147710_-intronic
ADediting_524579chr16_23147711_-intronic
ADediting_524580chr16_23147736_-intronic
ADediting_524581chr16_23147815_-intronic
ADediting_524582chr16_23147861_-intronic
ADediting_524583chr16_23147862_-intronic
ADediting_524585chr16_23147931_-intronic
ADediting_1541439chr16_23147311_-intronic
ADediting_1624068chr16_23126211_-intronic
ADediting_1624069chr16_23127184_-intronic
ADediting_1624070chr16_23127283_-intronic
ADediting_1624071chr16_23127327_-intronic
ADediting_1624072chr16_23127410_-intronic
ADediting_1624073chr16_23147284_-intronic
ADediting_1624074chr16_23147937_-intronic
ADediting_1624075chr16_23147942_-intronic
ADediting_1624076chr16_23147948_-intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_524471chr16_23117927_-SINEAluName=AluSz
ADediting_524472chr16_23118020_-SINEAluName=AluSz
ADediting_524473chr16_23118062_-SINEAluName=AluSz
ADediting_524474chr16_23118068_-SINEAluName=AluSz
ADediting_524475chr16_23118833_-SINEAluName=AluSx
ADediting_524476chr16_23118851_-SINEAluName=AluSx
ADediting_524477chr16_23118890_-SINEAluName=AluSx
ADediting_524478chr16_23118891_-SINEAluName=AluSx
ADediting_524479chr16_23118910_-SINEAluName=AluSx
ADediting_524480chr16_23118911_-SINEAluName=AluSx
ADediting_524481chr16_23119164_-SINEAluName=AluSz
ADediting_524482chr16_23119166_-SINEAluName=AluSz
ADediting_524483chr16_23119171_-SINEAluName=AluSz
ADediting_524484chr16_23119195_-SINEAluName=AluSz
ADediting_524485chr16_23119196_-SINEAluName=AluSz
ADediting_524486chr16_23119236_-SINEAluName=AluSz
ADediting_524487chr16_23119373_-SINEAluName=AluSz
ADediting_524488chr16_23119389_-SINEAluName=AluSz
ADediting_524496chr16_23127236_-SINEAluName=AluJb
ADediting_524498chr16_23127305_-SINEAluName=AluJb
ADediting_524499chr16_23127315_-SINEAluName=AluJb
ADediting_524500chr16_23127344_-SINEAluName=AluJb
ADediting_524501chr16_23127351_-SINEAluName=AluJb
ADediting_524502chr16_23127356_-SINEAluName=AluJb
ADediting_524503chr16_23127362_-SINEAluName=AluJb
ADediting_524504chr16_23127517_-SINEAluName=AluSg4
ADediting_524505chr16_23127555_-SINEAluName=AluSg4
ADediting_524506chr16_23127750_-SINEAluName=AluSg4
ADediting_524524chr16_23133929_-SINEAluName=AluJb
ADediting_524525chr16_23133947_-SINEAluName=AluJb
ADediting_524526chr16_23133994_-SINEAluName=AluJb
ADediting_524527chr16_23134063_-SINEAluName=AluJb
ADediting_524541chr16_23139319_-SINEAluName=AluSx
ADediting_524542chr16_23141470_-SINEAluName=AluJb
ADediting_524543chr16_23141485_-SINEAluName=AluJb
ADediting_524544chr16_23141506_-SINEAluName=AluJb
ADediting_524545chr16_23141571_-SINEAluName=AluJb
ADediting_524546chr16_23141578_-SINEAluName=AluJb
ADediting_524547chr16_23141595_-SINEAluName=AluJb
ADediting_524548chr16_23141596_-SINEAluName=AluJb
ADediting_524549chr16_23141649_-SINEAluName=AluJb
ADediting_524550chr16_23141650_-SINEAluName=AluJb
ADediting_524551chr16_23144527_-SINEAluName=AluSz6
ADediting_524552chr16_23144572_-SINEAluName=AluSz6
ADediting_524553chr16_23144576_-SINEAluName=AluSz6
ADediting_524554chr16_23144617_-SINEAluName=AluSz6
ADediting_524555chr16_23144754_-SINEAluName=AluSz6
ADediting_524556chr16_23144755_-SINEAluName=AluSz6
ADediting_524558chr16_23146416_-SINEAluName=AluYc
ADediting_524559chr16_23146437_-SINEAluName=AluYc
ADediting_524560chr16_23146481_-SINEAluName=AluYc
ADediting_524565chr16_23147134_-SINEAluName=AluSp
ADediting_524566chr16_23147144_-SINEAluName=AluSp
ADediting_524567chr16_23147181_-SINEAluName=AluSp
ADediting_524568chr16_23147205_-SINEAluName=AluSp
ADediting_524569chr16_23147220_-SINEAluName=AluSp
ADediting_524570chr16_23147233_-SINEAluName=AluSp
ADediting_524571chr16_23147237_-SINEAluName=AluSp
ADediting_524572chr16_23147246_-SINEAluName=AluSp
ADediting_524573chr16_23147255_-SINEAluName=AluSp
ADediting_524574chr16_23147341_-SINEAluName=AluSp
ADediting_524575chr16_23147381_-SINEAluName=AluSp
ADediting_524576chr16_23147382_-SINEAluName=AluSp
ADediting_524577chr16_23147682_-SINEAluName=AluJr
ADediting_524578chr16_23147710_-SINEAluName=AluJr
ADediting_524579chr16_23147711_-SINEAluName=AluJr
ADediting_524580chr16_23147736_-SINEAluName=AluJr
ADediting_524581chr16_23147815_-SINEAluName=AluJr
ADediting_524582chr16_23147861_-SINEAluName=AluJr
ADediting_524583chr16_23147862_-SINEAluName=AluJr
ADediting_524585chr16_23147931_-SINEAluName=AluJr
ADediting_1541439chr16_23147311_-SINEAluName=AluSp
ADediting_1624068chr16_23126211_-SINEAluName=AluJr
ADediting_1624069chr16_23127184_-SINEAluName=AluJb
ADediting_1624070chr16_23127283_-SINEAluName=AluJb
ADediting_1624071chr16_23127327_-SINEAluName=AluJb
ADediting_1624072chr16_23127410_-SINEAluName=AluJb
ADediting_1624073chr16_23147284_-SINEAluName=AluSp
ADediting_1624074chr16_23147937_-SINEAluName=AluJr
ADediting_1624075chr16_23147942_-SINEAluName=AluJr
ADediting_1624076chr16_23147948_-SINEAluName=AluJr

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RNA A-to-I editing events in the alternative splicing sites for USP31

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 USP31

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

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 USP31

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


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The effects of the RNA editing to the miRNA binding sites for USP31


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_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-589-3pchr1623063633230636397mer-m82306363223063656153-16.47
ADediting_1471003chr9_63819626_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-4477bchr1623063165230631717mer-m82306316423063190152-16.68
ADediting_1596844chr1_162342605_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-556-3pchr1623066696230667027mer-m82306669523066716154-13.1
ADediting_1596844chr1_162342605_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-556-3pchr1623067497230675037mer-m82306749623067517150-10.23
ADediting_1631458chr19_40282624_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-641chr1623061412230614187mer-m82306141123061437146-12.49
ADediting_843620chr2_207754818_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-4775chr1623065582230655887mer-m82306558123065603158-10.26

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_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-5688chr1623065144230651507mer-m82306514323065167155-12.49
ADediting_1337758chr7_5495892_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-589-5pchr1623064630230646367mer-m82306462923064652155-24.02
ADediting_1337758chr7_5495892_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-589-5pchr1623066119230661268mer-1a2306611923066140149-24.47
ADediting_1471003chr9_63819626_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-4477bchr1623065076230650827mer-m82306507523065095141-9.4
ADediting_1471004chr9_63819627_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-4477bchr1623065076230650827mer-m82306507523065095141-9.4
ADediting_1556067chr19_40282625_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-641chr1623061670230616767mer-m82306166923061692140-11.46
ADediting_1631458chr19_40282624_-ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-641chr1623061670230616767mer-m82306166923061692140-11.46
ADediting_1643790chr3_121049689_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-5682chr1623062014230620207mer-m82306201323062034153-17.17
ADediting_843620chr2_207754818_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-4775chr1623065265230652717mer-m82306526423065285153-11.08
ADediting_98288chr1_32086990_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-5585-3pchr1623061561230615677mer-1a2306156123061582145-15.35
ADediting_98289chr1_32086992_+ENSG00000103404.14ENST00000219689.11USP31-201hsa-miR-5585-3pchr1623061561230615677mer-1a2306156123061582145-15.35

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 USP31

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.
ENST00000219689.11protein_codingSoverviewSoverview
ENST00000567975.1protein_codingSoverviewSoverview

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
ADediting_524367ENST00000219689.11chr16_23068470_-3635-3356.10-3356.40-3356.10
ADediting_524367ENST00000567975.1chr16_23068470_-1651-744.70-745.00-744.70

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

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Relation with ADAR for USP31

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.)
DLPFC4.59174891877549e-310.5949315352314975.09110389965869e-250.5415304976179130.8158739074322270.0132783404607612
PCC6.29727255116145e-090.4048254505302171.32339494016125e-110.4643377254758950.006773885634486710.195318141223813
CER8.6667577676891e-370.814316229084752.80659781957546e-440.8561354508765250.0008024508210982610.270818082408589
TCX3.96718105072074e-220.6852638426401452.2838089910154e-060.3748870308717421.41890236235674e-090.468995672600104
FP6.72563271605631e-290.7126378530820993.06485293670574e-310.7327717249978041.44542864431919e-090.433887659370531
IFG3.85948619957162e-060.7821869560277511.13511064666728e-050.7580631507398140.0004549529642457520.648472804051514
PG1.11366262457252e-460.8210877700450195.38620830092896e-300.7113904639927720.02653476549724910.162664952255705
STG3.62454358230354e-110.6447516341799821.35074882732402e-080.571658523635510.0001617223439636940.400247594148225

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Relation with AD stages for USP31

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.
CER8.19138718265065e-060.414526934216031
TCX1.51352355252356e-080.515920393018064

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RelatedDrugs for USP31

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 USP31

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