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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 ELP3

check button Gene summary
Gene informationGene symbol

ELP3

Gene ID

55140

Gene nameelongator acetyltransferase complex subunit 3
SynonymsKAT9
Cytomap

8p21.1

Type of geneprotein-coding
Descriptionelongator complex protein 3elongation protein 3 homolog
Modification date20180523
UniProtAcc

Q9H9T3

ContextPubMed: ELP3 [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
ELP3

GO:0006357

regulation of transcription by RNA polymerase II

11818576

ELP3

GO:0043966

histone H3 acetylation

11714725

ELP3

GO:0043967

histone H4 acetylation

11714725


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Exon skipping events across known transcript of Ensembl for ELP3 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 ELP3

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 ELP3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_482456827947747:27947849:27954735:27954835:27957344:2795748327954735:27954835ENSG00000134014.12ENST00000521015.1
exon_skip_482457827947862:27947920:27954735:27954835:27957344:2795748327954735:27954835ENSG00000134014.12ENST00000521570.1
exon_skip_482459827950701:27950750:27954735:27954835:27957344:2795748327954735:27954835ENSG00000134014.12ENST00000256398.8,ENST00000521938.1,ENST00000523760.1
exon_skip_482461827954735:27954835:27957344:27957483:27964229:2796430027957344:27957483ENSG00000134014.12ENST00000521570.1,ENST00000256398.8,ENST00000521099.1,ENST00000520288.1,ENST00000520270.1,ENST00000521938.1,ENST00000521015.1,ENST00000523760.1
exon_skip_482462827964229:27964300:27965429:27965493:27967886:2796793927965429:27965493ENSG00000134014.12ENST00000521570.1,ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000524103.1,ENST00000520288.1,ENST00000522063.1,ENST00000521938.1,ENST00000521015.1,ENST00000523760.1
exon_skip_482463827965429:27965493:27967886:27967955:27970535:2797069027967886:27967955ENSG00000134014.12ENST00000521570.1,ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000524103.1,ENST00000521015.1,ENST00000523760.1
exon_skip_482464827967886:27967955:27970535:27970690:27987018:2798718027970535:27970690ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482467827987018:27987180:27989794:27989921:27995214:2799540827989794:27989921ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000520110.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482469827989794:27989921:27995214:27995408:28013458:2801354927995214:27995408ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000520110.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482472827995214:27995408:28013458:28013549:28016084:2801614228013458:28013549ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000520110.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482476828016114:28016150:28017745:28017973:28019513:2801959528017745:28017973ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000523357.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482477828017745:28017973:28019513:28019595:28047165:2804748928019513:28019595ENSG00000134014.12ENST00000380353.4,ENST00000256398.8,ENST00000518112.1,ENST00000542181.1,ENST00000537665.1,ENST00000523687.1,ENST00000524103.1,ENST00000519261.1,ENST00000521015.1
exon_skip_482478828019537:28019595:28040710:28040781:28047165:2804748928040710:28040781ENSG00000134014.12ENST00000523357.1

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

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Exon skipping events with PSIs in GTEx for ELP3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_482456827947747:27947849:27954735:27954835:27957344:2795748327954735:27954835ENSG00000134014.12ENST00000521015.1
exon_skip_482459827950701:27950750:27954735:27954835:27957344:2795748327954735:27954835ENSG00000134014.12ENST00000256398.8,ENST00000523760.1,ENST00000521938.1
exon_skip_482461827954735:27954835:27957344:27957483:27964229:2796430027957344:27957483ENSG00000134014.12ENST00000520270.1,ENST00000521015.1,ENST00000521570.1,ENST00000256398.8,ENST00000523760.1,ENST00000521938.1,ENST00000520288.1,ENST00000521099.1
exon_skip_482462827964229:27964300:27965429:27965493:27967886:2796793927965429:27965493ENSG00000134014.12ENST00000521015.1,ENST00000521570.1,ENST00000256398.8,ENST00000523760.1,ENST00000524103.1,ENST00000518112.1,ENST00000521938.1,ENST00000380353.4,ENST00000520288.1,ENST00000522063.1
exon_skip_482463827965429:27965493:27967886:27967955:27970535:2797069027967886:27967955ENSG00000134014.12ENST00000521015.1,ENST00000521570.1,ENST00000256398.8,ENST00000523760.1,ENST00000524103.1,ENST00000518112.1,ENST00000380353.4
exon_skip_482464827967886:27967955:27970535:27970690:27987018:2798718027970535:27970690ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4
exon_skip_482467827987018:27987180:27989794:27989921:27995214:2799540827989794:27989921ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4,ENST00000520110.1
exon_skip_482469827989794:27989921:27995214:27995408:28013458:2801354927995214:27995408ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4,ENST00000520110.1
exon_skip_482472827995214:27995408:28013458:28013549:28016084:2801614228013458:28013549ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4,ENST00000520110.1
exon_skip_482476828016114:28016150:28017745:28017973:28019513:2801959528017745:28017973ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4,ENST00000523357.1
exon_skip_482477828017745:28017973:28019513:28019595:28047165:2804748928019513:28019595ENSG00000134014.12ENST00000521015.1,ENST00000256398.8,ENST00000523687.1,ENST00000542181.1,ENST00000524103.1,ENST00000518112.1,ENST00000519261.1,ENST00000537665.1,ENST00000380353.4
exon_skip_482478828019537:28019595:28040710:28040781:28047165:2804748928040710:28040781ENSG00000134014.12ENST00000523357.1

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 ELP3

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
ENST000002563982795473527954835Frame-shift
ENST000002563982795734427957483Frame-shift
ENST000002563982796542927965493Frame-shift
ENST000002563982797053527970690Frame-shift
ENST000002563982798979427989921Frame-shift
ENST000002563982799521427995408Frame-shift
ENST000002563982801345828013549Frame-shift
ENST000002563982801951328019595Frame-shift
ENST000002563982796788627967955In-frame
ENST000002563982801774528017973In-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
ENST000002563982795473527954835Frame-shift
ENST000002563982795734427957483Frame-shift
ENST000002563982796542927965493Frame-shift
ENST000002563982797053527970690Frame-shift
ENST000002563982798979427989921Frame-shift
ENST000002563982799521427995408Frame-shift
ENST000002563982801345828013549Frame-shift
ENST000002563982801951328019595Frame-shift
ENST000002563982796788627967955In-frame
ENST000002563982801774528017973In-frame

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Infer the effects of exon skipping event on protein functional features for ELP3

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
ENST0000025639834695472796788627967955771839131154
ENST000002563983469547280177452801797316351862419495

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
ENST0000025639834695472796788627967955771839131154
ENST000002563983469547280177452801797316351862419495

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
Q9H9T313115413131Alternative sequenceID=VSP_055286;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H9T31311541547ChainID=PRO_0000283986;Note=Elongator complex protein 3
Q9H9T34194951547ChainID=PRO_0000283986;Note=Elongator complex protein 3
Q9H9T3419495396547DomainNote=N-acetyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00532


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
Q9H9T313115413131Alternative sequenceID=VSP_055286;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H9T31311541547ChainID=PRO_0000283986;Note=Elongator complex protein 3
Q9H9T34194951547ChainID=PRO_0000283986;Note=Elongator complex protein 3
Q9H9T3419495396547DomainNote=N-acetyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00532


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SNVs in the skipped exons for ELP3

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.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
COADTCGA-AZ-6598-01exon_skip_482467
27989795279899212798992127989924Frame_Shift_DelAGTA-p.302_302del
BRCATCGA-E2-A109-01exon_skip_482469
27995215279954082799526727995267Frame_Shift_DelC-p.L321fs
LIHCTCGA-DD-A39Y-01exon_skip_482469
27995215279954082799529127995291Frame_Shift_DelT-p.L328fs
LIHCTCGA-DD-A39Y-01exon_skip_482476
28017746280179732801782528017825Frame_Shift_DelT-p.I446fs
STADTCGA-BR-7197-01exon_skip_482463
27967887279679552796792727967928Frame_Shift_Ins-CCTAp.F145fs
STADTCGA-BR-7197-01exon_skip_482463
27967887279679552796792827967929Frame_Shift_Ins-CCTAp.F145fs
UCECTCGA-BS-A0UF-01exon_skip_482464
27970536279706902797061127970611Nonsense_MutationGTp.E180*
UCECTCGA-AP-A056-01exon_skip_482464
27970536279706902797063227970632Nonsense_MutationCTp.R187*
UCECTCGA-AX-A05Z-01exon_skip_482464
27970536279706902797063227970632Nonsense_MutationCTp.R187*
LIHCTCGA-XR-A8TF-01exon_skip_482461
27957345279574832795734327957343Splice_SiteAT.
STADTCGA-F1-A448-01exon_skip_482469
27995215279954082799541027995410Splice_SiteTCp.R367_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
ELP3_27967886_27967955_27970535_27970690_27987018_27987180_TCGA-BS-A0UF-01Sample: TCGA-BS-A0UF-01
Cancer type: UCEC
ESID: exon_skip_482464
Skipped exon start: 27970536
Skipped exon end: 27970690
Mutation start: 27970611
Mutation end: 27970611
Mutation type: Nonsense_Mutation
Reference seq: G
Mutation seq: T
AAchange: p.E180*
exon_skip_104037_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_105868_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_105985_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_115426_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_14705_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_147467_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_19372_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_286379_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_294437_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_321837_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_324767_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_345944_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_345950_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_382354_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_389258_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_389265_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_39691_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_40297_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_461887_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_482464_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_59390_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_82288_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_84605_UCEC_TCGA-BS-A0UF-01.png
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exon_skip_95240_UCEC_TCGA-BS-A0UF-01.png
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check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNU1040_LARGE_INTESTINE27957345279574832795739227957392Missense_MutationGAp.R56H
NCIH2291_LUNG27957345279574832795742727957427Missense_MutationTGp.Y68D
SNU1040_LARGE_INTESTINE27957345279574832795743127957431Missense_MutationGAp.R69H
HCC515_LUNG27965430279654932796544127965441Missense_MutationGAp.G114D
GP2D_LARGE_INTESTINE27970536279706902797058427970584Missense_MutationGAp.G171S
GP5D_LARGE_INTESTINE27970536279706902797058427970584Missense_MutationGAp.G171S
D336MG_CENTRAL_NERVOUS_SYSTEM27970536279706902797063827970638Missense_MutationTAp.L189I
TT_OESOPHAGUS27989795279899212798984827989848Missense_MutationGCp.G278A
HEC1A_ENDOMETRIUM27989795279899212798987427989874Missense_MutationCTp.P287S
HEC1_ENDOMETRIUM27989795279899212798987427989874Missense_MutationCTp.P287S
HEC1B_ENDOMETRIUM27989795279899212798987427989874Missense_MutationCTp.P287S
MET2B27995215279954082799523927995239Missense_MutationCTp.R311C
MM370_SKIN27995215279954082799530927995309Missense_MutationCTp.S334L
TT2609C02_THYROID27995215279954082799539027995390Missense_MutationGAp.R361Q
SNU520_STOMACH28017746280179732801780328017803Missense_MutationTCp.Y439H
HUH7_LIVER28019514280195952801954128019541Missense_MutationGAp.A505T
OPM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28019514280195952801955328019553Missense_MutationGCp.A509P
MEWO_SKIN28019514280195952801955928019559Missense_MutationGAp.E511K
UMC11_LUNG27965430279654932796543627965436Nonsense_MutationCAp.C112*
JHUEM7_ENDOMETRIUM27989795279899212798991027989910Nonsense_MutationGTp.E299*
HPAFII_PANCREAS27995215279954082799525427995254Nonsense_MutationATp.K316*
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE27995215279954082799539827995398Nonsense_MutationCTp.R364*
LNCAPCLONEFGC_PROSTATE28017746280179732801784228017842Nonsense_MutationCTp.R452*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ELP3

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 ELP3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ELP3


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RelatedDrugs for ELP3

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 ELP3

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