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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 DENND1A

check button Gene summary
Gene informationGene symbol

DENND1A

Gene ID

57706

Gene nameDENN domain containing 1A
SynonymsFAM31A|KIAA1608
Cytomap

9q33.3

Type of geneprotein-coding
DescriptionDENN domain-containing protein 1ADENN/MADD domain containing 1Aconnecdenn 1
Modification date20180523
UniProtAcc

Q8TEH3

ContextPubMed: DENND1A [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
DENND1A

GO:0032483

regulation of Rab protein signal transduction

20937701


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Exon skipping events across known transcript of Ensembl for DENND1A 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 DENND1A

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 DENND1A

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_5067469126145933:126146192:126150008:126150137:126165680:126165769126150008:126150137ENSG00000119522.11ENST00000542603.1,ENST00000473039.1,ENST00000394219.3
exon_skip_5067549126202638:126202770:126212971:126213028:126214554:126214622126212971:126213028ENSG00000119522.11ENST00000479305.1,ENST00000542603.1,ENST00000473039.1,ENST00000497135.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000491650.1,ENST00000373618.1,ENST00000394215.2
exon_skip_5067649126214554:126214626:126217017:126217058:126219626:126219657126217017:126217058ENSG00000119522.11ENST00000479305.1,ENST00000542603.1,ENST00000497135.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000462245.1,ENST00000394215.2
exon_skip_5067659126217017:126217058:126219125:126219210:126219626:126219714126219125:126219210ENSG00000119522.11ENST00000491650.1
exon_skip_5067669126217017:126217058:126219626:126219714:126220071:126220176126219626:126219714ENSG00000119522.11ENST00000479305.1,ENST00000542603.1,ENST00000497135.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2
exon_skip_5067689126220071:126220176:126319848:126319974:126345447:126345496126319848:126319974ENSG00000119522.11ENST00000497135.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000491650.1,ENST00000373618.1,ENST00000394215.2
exon_skip_5067699126345447:126345549:126371714:126371760:126392654:126392755126371714:126371760ENSG00000119522.11ENST00000542603.1,ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2,ENST00000474676.1
exon_skip_5067729126371714:126371760:126392654:126392755:126414291:126414330126392654:126392755ENSG00000119522.11ENST00000542603.1,ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2,ENST00000474676.1
exon_skip_5067769126392674:126392755:126414291:126414402:126429304:126429358126414291:126414402ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2,ENST00000474676.1
exon_skip_5067779126414291:126414402:126429304:126429358:126433569:126433650126429304:126429358ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2,ENST00000474676.1
exon_skip_5067799126429304:126429358:126433569:126433650:126438998:126439068126433569:126433650ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2
exon_skip_5067809126429304:126429358:126433569:126433650:126519981:126520038126433569:126433650ENSG00000119522.11ENST00000473039.1,ENST00000474676.1
exon_skip_5067829126433569:126433650:126438998:126439068:126519981:126520038126438998:126439068ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000373618.1,ENST00000394215.2
exon_skip_5067849126438998:126439068:126519981:126520101:126531792:126531842126519981:126520101ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2
exon_skip_5067859126438998:126439068:126519981:126520101:126554865:126554909126519981:126520101ENSG00000119522.11ENST00000373618.1
exon_skip_5067879126519981:126520101:126531792:126531842:126554865:126554909126531792:126531842ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000373620.3
exon_skip_5067889126519981:126520101:126531792:126531842:126641229:126641300126531792:126531842ENSG00000119522.11ENST00000394215.2
exon_skip_5067899126519981:126520101:126554865:126554909:126641229:126641300126554865:126554909ENSG00000119522.11ENST00000373618.1
exon_skip_5067909126531792:126531842:126554865:126554909:126641229:126641296126554865:126554909ENSG00000119522.11ENST00000373624.2,ENST00000373620.3
exon_skip_5067939126531792:126531842:126641229:126641300:126692167:126692393126641229:126641300ENSG00000119522.11ENST00000394215.2
exon_skip_5067959126554865:126554909:126641229:126641300:126692167:126692386126641229:126641300ENSG00000119522.11ENST00000373624.2,ENST00000373620.3,ENST00000373618.1

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

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Exon skipping events with PSIs in GTEx for DENND1A

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_5067469126145933:126146192:126150008:126150137:126165680:126165769126150008:126150137ENSG00000119522.11ENST00000473039.1,ENST00000542603.1,ENST00000394219.3
exon_skip_5067549126202638:126202770:126212971:126213028:126214554:126214622126212971:126213028ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000542603.1,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000491650.1,ENST00000497135.1,ENST00000373618.1,ENST00000479305.1
exon_skip_5067649126214554:126214626:126217017:126217058:126219626:126219657126217017:126217058ENSG00000119522.11ENST00000373624.2,ENST00000542603.1,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000497135.1,ENST00000373618.1,ENST00000479305.1,ENST00000462245.1
exon_skip_5067669126217017:126217058:126219626:126219714:126220071:126220176126219626:126219714ENSG00000119522.11ENST00000373624.2,ENST00000542603.1,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000497135.1,ENST00000373618.1,ENST00000479305.1
exon_skip_5067689126220071:126220176:126319848:126319974:126345447:126345496126319848:126319974ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000491650.1,ENST00000497135.1,ENST00000373618.1
exon_skip_5067699126345447:126345549:126371714:126371760:126392654:126392755126371714:126371760ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000542603.1,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1,ENST00000474676.1
exon_skip_5067729126371714:126371760:126392654:126392755:126414291:126414330126392654:126392755ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000542603.1,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1,ENST00000474676.1
exon_skip_5067769126392674:126392755:126414291:126414402:126429304:126429358126414291:126414402ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1,ENST00000474676.1
exon_skip_5067779126414291:126414402:126429304:126429358:126433569:126433650126429304:126429358ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1,ENST00000474676.1
exon_skip_5067799126429304:126429358:126433569:126433650:126438998:126439068126433569:126433650ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1
exon_skip_5067809126429304:126429358:126433569:126433650:126519981:126520038126433569:126433650ENSG00000119522.11ENST00000473039.1,ENST00000474676.1
exon_skip_5067829126433569:126433650:126438998:126439068:126519981:126520038126438998:126439068ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2,ENST00000373618.1
exon_skip_5067849126438998:126439068:126519981:126520101:126531792:126531842126519981:126520101ENSG00000119522.11ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2
exon_skip_5067859126438998:126439068:126519981:126520101:126554865:126554909126519981:126520101ENSG00000119522.11ENST00000373618.1
exon_skip_5067879126519981:126520101:126531792:126531842:126554865:126554909126531792:126531842ENSG00000119522.11ENST00000473039.1,ENST00000373624.2,ENST00000373620.3
exon_skip_5067889126519981:126520101:126531792:126531842:126641229:126641300126531792:126531842ENSG00000119522.11ENST00000394215.2
exon_skip_5067899126519981:126520101:126554865:126554909:126641229:126641300126554865:126554909ENSG00000119522.11ENST00000373618.1
exon_skip_5067909126531792:126531842:126554865:126554909:126641229:126641296126554865:126554909ENSG00000119522.11ENST00000373624.2,ENST00000373620.3
exon_skip_5067939126531792:126531842:126641229:126641300:126692167:126692393126641229:126641300ENSG00000119522.11ENST00000394215.2
exon_skip_5067959126554865:126554909:126641229:126641300:126692167:126692386126641229:126641300ENSG00000119522.11ENST00000373624.2,ENST00000373620.3,ENST00000373618.1

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 DENND1A

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
ENST00000373624126217017126217058Frame-shift
ENST00000373624126219626126219714Frame-shift
ENST00000373624126371714126371760Frame-shift
ENST00000373624126392654126392755Frame-shift
ENST00000373624126438998126439068Frame-shift
ENST00000373624126531792126531842Frame-shift
ENST00000373624126554865126554909Frame-shift
ENST00000373624126641229126641300Frame-shift
ENST00000373624126212971126213028In-frame
ENST00000373624126319848126319974In-frame
ENST00000373624126414291126414402In-frame
ENST00000373624126429304126429358In-frame
ENST00000373624126433569126433650In-frame
ENST00000373624126519981126520101In-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
ENST00000373624126217017126217058Frame-shift
ENST00000373624126219626126219714Frame-shift
ENST00000373624126371714126371760Frame-shift
ENST00000373624126392654126392755Frame-shift
ENST00000373624126438998126439068Frame-shift
ENST00000373624126531792126531842Frame-shift
ENST00000373624126554865126554909Frame-shift
ENST00000373624126641229126641300Frame-shift
ENST00000373624126212971126213028In-frame
ENST00000373624126319848126319974In-frame
ENST00000373624126414291126414402In-frame
ENST00000373624126429304126429358In-frame
ENST00000373624126433569126433650In-frame
ENST00000373624126519981126520101In-frame

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Infer the effects of exon skipping event on protein functional features for DENND1A

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
ENST000003736245027100912651998112652010138550461100
ENST0000037362450271009126433569126433650575655124151
ENST0000037362450271009126429304126429358656709151169
ENST0000037362450271009126414291126414402710820169206
ENST000003736245027100912631984812631997410701195289331
ENST000003736245027100912621297112621302815021558433452

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
ENST000003736245027100912651998112652010138550461100
ENST0000037362450271009126433569126433650575655124151
ENST0000037362450271009126429304126429358656709151169
ENST0000037362450271009126414291126414402710820169206
ENST000003736245027100912631984812631997410701195289331
ENST000003736245027100912621297112621302815021558433452

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


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


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SNVs in the skipped exons for DENND1A

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
LIHCTCGA-G3-A3CJ-01exon_skip_506754
126212972126213028126212988126212988Frame_Shift_DelT-p.N447fs
LIHCTCGA-G3-A3CJ-01exon_skip_506754
126212972126213028126213006126213006Frame_Shift_DelC-p.G441fs
STADTCGA-BR-8078-01exon_skip_506768
126319849126319974126319868126319868Frame_Shift_DelT-p.N325fs
LIHCTCGA-DD-A39Y-01exon_skip_506777
126429305126429358126429339126429339Frame_Shift_DelG-p.P158fs
SKCMTCGA-EE-A29M-06exon_skip_506766
126219627126219714126219702126219702Nonsense_MutationGAp.R371*
LGGTCGA-DU-6392-01exon_skip_506769
126371715126371760126371738126371738Nonsense_MutationCAp.G248*
LUSCTCGA-33-4532-01exon_skip_506776
126414292126414402126414402126414402Nonsense_MutationTAp.R138_splice
UCECTCGA-BS-A0UF-01exon_skip_506777
126429305126429358126429350126429350Nonsense_MutationACp.Y154*
LUADTCGA-35-4122-01exon_skip_506793
exon_skip_506795
126641230126641300126641232126641232Nonsense_MutationGAp.Q14*
BRCATCGA-AN-A0AR-01exon_skip_506769
126371715126371760126371761126371761Splice_SiteCGe11-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
FLO1_OESOPHAGUS126212972126213028126213024126213024Missense_MutationTAp.K435I
HEC6_ENDOMETRIUM126219627126219714126219636126219636Missense_MutationCTp.E393K
SCC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE126319849126319974126319866126319866Missense_MutationCGp.A326P
HCC2998_LARGE_INTESTINE126319849126319974126319898126319898Missense_MutationGAp.A315V
SNU1_STOMACH126319849126319974126319946126319946Missense_MutationTCp.K299R
MEWO_SKIN126371715126371760126371732126371732Missense_MutationGAp.H250Y
IPC298_SKIN126392655126392755126392665126392665Missense_MutationCAp.D237Y
JHUEM1_ENDOMETRIUM126392655126392755126392737126392737Missense_MutationCTp.G213R
HCT15_LARGE_INTESTINE126414292126414402126414332126414332Missense_MutationTCp.Y193C
SNU1040_LARGE_INTESTINE126414292126414402126414362126414362Missense_MutationTCp.N183S
SNUC5_LARGE_INTESTINE126429305126429358126429313126429313Missense_MutationGAp.P167S
YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE126433570126433650126433610126433610Missense_MutationAGp.L138P
NCIH720_LUNG126433570126433650126433626126433626Missense_MutationCGp.E133Q
NB1_AUTONOMIC_GANGLIA126519982126520101126520064126520064Missense_MutationCAp.V74L
LNCAPCLONEFGC_PROSTATE126641230126641300126641241126641241Missense_MutationCTp.G26D
NCIH1693_LUNG126641230126641300126641250126641250Missense_MutationCAp.R23M
NCIH1819_LUNG126641230126641300126641250126641250Missense_MutationCAp.R23M
SNU1040_LARGE_INTESTINE126319849126319974126319872126319872Nonsense_MutationGAp.R324*
HT115_LARGE_INTESTINE126414292126414402126414401126414401Splice_SiteCTp.R170K

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for DENND1A

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_5067859126438998:126439068:126519981:126520101:126554865:126554909126519981:126520101ENST00000373618.1COADrs9785285chr9:126520068T/C2.00e-03
exon_skip_5067859126438998:126439068:126519981:126520101:126554865:126554909126519981:126520101ENST00000373618.1LGGrs9785285chr9:126520068T/C7.56e-04
exon_skip_5067849126438998:126439068:126519981:126520101:126531792:126531842126519981:126520101ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2COADrs9785285chr9:126520068T/C2.00e-03
exon_skip_5067849126438998:126439068:126519981:126520101:126531792:126531842126519981:126520101ENST00000373624.2,ENST00000394219.3,ENST00000373620.3,ENST00000394215.2LGGrs9785285chr9:126520068T/C7.56e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DENND1A


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for DENND1A


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RelatedDrugs for DENND1A

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 DENND1A

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