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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for USP25

check button Gene summary
Gene informationGene symbol

USP25

Gene ID

29761

Gene nameubiquitin specific peptidase 25
SynonymsUSP21
Cytomap

21q21.1

Type of geneprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase 25USP on chromosome 21deubiquitinating enzyme 25ubiquitin thioesterase 25ubiquitin thiolesterase 25ubiquitin-specific processing protease 25
Modification date20180523
UniProtAcc

Q9UHP3

ContextPubMed: USP25 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
USP25

GO:0016579

protein deubiquitination

22590560


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Exon skipping events across known transcript of Ensembl for USP25 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for USP25

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for USP25

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3589132117102495:17102757:17135209:17135287:17138315:1713846017135209:17135287ENSG00000155313.11ENST00000400183.2,ENST00000351097.5,ENST00000285681.2
exon_skip_3589202117138320:17138460:17150222:17150346:17163820:1716398317150222:17150346ENSG00000155313.11ENST00000400183.2,ENST00000285679.6,ENST00000351097.5,ENST00000285681.2
exon_skip_3589282117163822:17163983:17172075:17172162:17177439:1717757717172075:17172162ENSG00000155313.11ENST00000547201.1,ENST00000400183.2,ENST00000285679.6,ENST00000351097.5,ENST00000285681.2,ENST00000549362.1
exon_skip_3589292117177439:17177577:17181127:17181204:17183455:1718352917181127:17181204ENSG00000155313.11ENST00000547201.1,ENST00000400183.2,ENST00000285679.6,ENST00000285681.2
exon_skip_3589372117191016:17191165:17196357:17196485:17197284:1719738017196357:17196485ENSG00000155313.11ENST00000400183.2,ENST00000285679.6,ENST00000285681.2
exon_skip_3589392117197328:17197380:17198522:17198684:17199295:1719952217198522:17198684ENSG00000155313.11ENST00000400183.2,ENST00000285679.6,ENST00000285681.2
exon_skip_3589412117199295:17199522:17202849:17202920:17203719:1720394817202849:17202920ENSG00000155313.11ENST00000453553.1,ENST00000400183.2,ENST00000285679.6,ENST00000285681.2
exon_skip_3589472117203719:17203948:17205666:17205867:17214716:1721485917205666:17205867ENSG00000155313.11ENST00000400183.2,ENST00000285679.6,ENST00000285681.2
exon_skip_3589532117205666:17205867:17214716:17214859:17236586:1723676517214716:17214859ENSG00000155313.11ENST00000285679.6
exon_skip_3589552117214836:17214859:17219981:17220095:17222095:1722219117219981:17220095ENSG00000155313.11ENST00000400183.2,ENST00000449491.1
exon_skip_3589582117214836:17214859:17222095:17222191:17236586:1723676517222095:17222191ENSG00000155313.11ENST00000285681.2
exon_skip_3589602117214836:17214859:17236586:17236765:17238584:1723866317236586:17236765ENSG00000155313.11ENST00000285679.6
exon_skip_3589612117219981:17220095:17222095:17222191:17236586:1723676517222095:17222191ENSG00000155313.11ENST00000400183.2,ENST00000449491.1
exon_skip_3589632117242386:17242466:17246721:17246845:17250114:1725031017246721:17246845ENSG00000155313.11ENST00000400183.2,ENST00000285679.6,ENST00000351097.5,ENST00000285681.2

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for USP25

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3589132117102495:17102757:17135209:17135287:17138315:1713846017135209:17135287ENSG00000155313.11ENST00000351097.5,ENST00000285681.2,ENST00000400183.2
exon_skip_3589202117138320:17138460:17150222:17150346:17163820:1716398317150222:17150346ENSG00000155313.11ENST00000285679.6,ENST00000351097.5,ENST00000285681.2,ENST00000400183.2
exon_skip_3589282117163822:17163983:17172075:17172162:17177439:1717757717172075:17172162ENSG00000155313.11ENST00000285679.6,ENST00000351097.5,ENST00000285681.2,ENST00000400183.2,ENST00000547201.1,ENST00000549362.1
exon_skip_3589292117177439:17177577:17181127:17181204:17183455:1718352917181127:17181204ENSG00000155313.11ENST00000285679.6,ENST00000285681.2,ENST00000400183.2,ENST00000547201.1
exon_skip_3589372117191016:17191165:17196357:17196485:17197284:1719738017196357:17196485ENSG00000155313.11ENST00000285679.6,ENST00000285681.2,ENST00000400183.2
exon_skip_3589392117197328:17197380:17198522:17198684:17199295:1719952217198522:17198684ENSG00000155313.11ENST00000285679.6,ENST00000285681.2,ENST00000400183.2
exon_skip_3589412117199295:17199522:17202849:17202920:17203719:1720394817202849:17202920ENSG00000155313.11ENST00000285679.6,ENST00000285681.2,ENST00000400183.2,ENST00000453553.1
exon_skip_3589472117203719:17203948:17205666:17205867:17214716:1721485917205666:17205867ENSG00000155313.11ENST00000285679.6,ENST00000285681.2,ENST00000400183.2
exon_skip_3589532117205666:17205867:17214716:17214859:17236586:1723676517214716:17214859ENSG00000155313.11ENST00000285679.6
exon_skip_3589552117214836:17214859:17219981:17220095:17222095:1722219117219981:17220095ENSG00000155313.11ENST00000400183.2,ENST00000449491.1
exon_skip_3589582117214836:17214859:17222095:17222191:17236586:1723676517222095:17222191ENSG00000155313.11ENST00000285681.2
exon_skip_3589602117214836:17214859:17236586:17236765:17238584:1723866317236586:17236765ENSG00000155313.11ENST00000285679.6
exon_skip_3589612117219981:17220095:17222095:17222191:17236586:1723676517222095:17222191ENSG00000155313.11ENST00000400183.2,ENST00000449491.1
exon_skip_3589632117242386:17242466:17246721:17246845:17250114:1725031017246721:17246845ENSG00000155313.11ENST00000285679.6,ENST00000351097.5,ENST00000285681.2,ENST00000400183.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for USP25

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002856811715022217150346Frame-shift
ENST000002856811718112717181204Frame-shift
ENST000002856811719635717196485Frame-shift
ENST000002856811720284917202920Frame-shift
ENST000002856811724672117246845Frame-shift
ENST000002856811713520917135287In-frame
ENST000002856811717207517172162In-frame
ENST000002856811719852217198684In-frame
ENST000002856811720566617205867In-frame
ENST000002856811722209517222191In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002856811715022217150346Frame-shift
ENST000002856811718112717181204Frame-shift
ENST000002856811719635717196485Frame-shift
ENST000002856811720284917202920Frame-shift
ENST000002856811724672117246845Frame-shift
ENST000002856811713520917135287In-frame
ENST000002856811717207517172162In-frame
ENST000002856811719852217198684In-frame
ENST000002856811720566617205867In-frame
ENST000002856811722209517222191In-frame

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Infer the effects of exon skipping event on protein functional features for USP25

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002856815233105517135209171352874154921541
ENST000002856815233105517172075171721629251011185214
ENST0000028568152331055171985221719868416741835435488
ENST0000028568152331055172056661720586723632563664731
ENST0000028568152331055172220951722219127072802779811

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002856815233105517135209171352874154921541
ENST000002856815233105517172075171721629251011185214
ENST0000028568152331055171985221719868416741835435488
ENST0000028568152331055172056661720586723632563664731
ENST0000028568152331055172220951722219127072802779811

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q9UHP3154111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP315411457DomainNote=UBA-like
Q9UHP315411227HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2MUX
Q9UHP315413343HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2MUX
Q9UHP318521411055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3185214169657DomainNote=USP
Q9UHP343548811055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3435488169657DomainNote=USP
Q9UHP366473111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3664731684717Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q9UHP3779811779779Alternative sequenceID=VSP_039632;Note=In isoform USP25b. S->SIMMTPNMQGIIMAIGKSRSVYDRCGPEAGFFK;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10644437;Dbxref=PMID:10644437
Q9UHP3779811779779Alternative sequenceID=VSP_039631;Note=In isoform USP25m. S->SKPENTTSQPLSNQRVVEVAIPHVGKFMIESKEGGYDDEIMMTPNMQGIIMAIGKSRSVYDRCGPEAGFFK;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.3
Q9UHP377981111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q9UHP3154111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP315411457DomainNote=UBA-like
Q9UHP315411227HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2MUX
Q9UHP315413343HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2MUX
Q9UHP318521411055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3185214169657DomainNote=USP
Q9UHP343548811055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3435488169657DomainNote=USP
Q9UHP366473111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25
Q9UHP3664731684717Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q9UHP3779811779779Alternative sequenceID=VSP_039632;Note=In isoform USP25b. S->SIMMTPNMQGIIMAIGKSRSVYDRCGPEAGFFK;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10644437;Dbxref=PMID:10644437
Q9UHP3779811779779Alternative sequenceID=VSP_039631;Note=In isoform USP25m. S->SKPENTTSQPLSNQRVVEVAIPHVGKFMIESKEGGYDDEIMMTPNMQGIIMAIGKSRSVYDRCGPEAGFFK;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.3
Q9UHP377981111055ChainID=PRO_0000080653;Note=Ubiquitin carboxyl-terminal hydrolase 25


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SNVs in the skipped exons for USP25

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
USP25_READ_exon_skip_358963_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-BC-A3KG-01exon_skip_358953
17214717172148591721475717214757Frame_Shift_DelA-p.S745fs
UCECTCGA-BS-A0UF-01exon_skip_358913
17135210171352871713524017135240Nonsense_MutationGTp.E26*
BLCATCGA-2F-A9KT-01exon_skip_358920
17150223171503461715026117150261Nonsense_MutationCTp.Q103*
DLBCTCGA-GR-7353-01exon_skip_358929
17181128171812041718116817181168Nonsense_MutationTGp.L274X
LUADTCGA-50-5946-01exon_skip_358937
17196358171964851719642717196427Nonsense_MutationGTp.G384*
THYMTCGA-XU-AAXX-01exon_skip_358939
17198523171986841719858717198587Nonsense_MutationGTp.E457X
COADTCGA-AD-6889-01exon_skip_358947
17205667172058671720575617205756Nonsense_MutationCTp.R695X
PAADTCGA-2J-AABT-01exon_skip_358947
17205667172058671720584317205843Nonsense_MutationGTp.E724*
LUADTCGA-17-Z026-01exon_skip_358953
17214717172148591721481617214816Nonsense_MutationCGp.S765*
LUSCTCGA-60-2713-01exon_skip_358953
17214717172148591721484217214842Nonsense_MutationGTp.E774*
READTCGA-F5-6814-01exon_skip_358963
17246722172468451724681017246810Nonsense_MutationGTp.E922X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
USP25_17242386_17242466_17246721_17246845_17250114_17250310_TCGA-F5-6814-01Sample: TCGA-F5-6814-01
Cancer type: READ
ESID: exon_skip_358963
Skipped exon start: 17246722
Skipped exon end: 17246845
Mutation start: 17246810
Mutation end: 17246810
Mutation type: Nonsense_Mutation
Reference seq: G
Mutation seq: T
AAchange: p.E922X
exon_skip_104037_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_108731_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_111139_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_111141_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_134785_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_138676_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_141979_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_142361_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_142369_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_142374_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_145114_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_145115_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_153669_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_28270_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_290191_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_296525_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_358963_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_428765_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_43545_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_444150_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_479241_READ_TCGA-F5-6814-01.png
boxplot
exon_skip_497224_READ_TCGA-F5-6814-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
BICR18_UPPER_AERODIGESTIVE_TRACT17246722172468451724678817246789Frame_Shift_DelCT-p.L915fs
DBTRG05MG_CENTRAL_NERVOUS_SYSTEM17236587172367651723667017236671In_Frame_Ins-GTGp.808_808V>VV
UMCHOR1_BONE17135210171352871713522017135220Missense_MutationCAp.T19K
HEC251_ENDOMETRIUM17135210171352871713525617135256Missense_MutationACp.N31T
KYSE520_OESOPHAGUS17135210171352871713527517135275Missense_MutationGTp.Q37H
NCIH1651_LUNG17150223171503461715023417150234Missense_MutationCTp.L94F
HEC6_ENDOMETRIUM17150223171503461715028817150288Missense_MutationGAp.E112K
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17172076171721621717214817172148Missense_MutationCAp.P210T
SNU81_LARGE_INTESTINE17172076171721621717215217172152Missense_MutationGAp.R211Q
SNU81_LARGE_INTESTINE17181128171812041718116117181161Missense_MutationGTp.D272Y
22RV1_PROSTATE17181128171812041718119917181199Missense_MutationGTp.E284D
DU145_PROSTATE17196358171964851719638917196389Missense_MutationCTp.T371I
JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17196358171964851719646417196464Missense_MutationCGp.P396R
SKMEL1_SKIN17198523171986841719853117198531Missense_MutationGCp.S438T
HCC2450_LUNG17198523171986841719857217198572Missense_MutationCTp.L452F
CORL95_LUNG17198523171986841719857617198576Missense_MutationAGp.Q453R
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17198523171986841719861517198615Missense_MutationCGp.T466S
HT115_LARGE_INTESTINE17202850172029201720288017202880Missense_MutationGAp.R575Q
SNU1040_LARGE_INTESTINE17202850172029201720288017202880Missense_MutationGAp.R575Q
BCPAP_THYROID17202850172029201720289417202894Missense_MutationAGp.M580V
MZ1PC_PANCREAS17205667172058671720569617205696Missense_MutationCTp.L675F
KOSC2_UPPER_AERODIGESTIVE_TRACT17205667172058671720582617205826Missense_MutationCTp.A718V
NKL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE17205667172058671720586217205862Missense_MutationCTp.T730I
SW756_CERVIX17214717172148591721476217214762Missense_MutationGAp.S747N
SNU1040_LARGE_INTESTINE17214717172148591721482217214822Missense_MutationAGp.E767G
GAK_SKIN17214717172148591721484017214840Missense_MutationCTp.P773L
HN_UPPER_AERODIGESTIVE_TRACT17214717172148591721484017214840Missense_MutationCTp.P773L
RKO_LARGE_INTESTINE17236587172367651723673717236737Missense_MutationGCp.G830R
NCIH2291_LUNG17246722172468451724682217246822Missense_MutationCTp.H926Y
HEC251_ENDOMETRIUM17135210171352871713524017135240Nonsense_MutationGTp.E26*
SH4_SKIN17196358171964851719646517196466Nonsense_MutationCCTTp.Q397*
SNU81_LARGE_INTESTINE17205667172058671720568117205681Nonsense_MutationGTp.E670*
EVSAT_BREAST17214717172148591721482717214827Nonsense_MutationGTp.E769*
CP50EBV_MATCHED_NORMAL_TISSUE17202850172029201720292017202920Splice_SiteAGp.Q588Q
CP50MELB_SKIN17202850172029201720292017202920Splice_SiteAGp.Q588Q

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for USP25

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USP25


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USP25


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RelatedDrugs for USP25

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 USP25

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