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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 CCDC88A

check button Gene summary
Gene informationGene symbol

CCDC88A

Gene ID

55704

Gene namecoiled-coil domain containing 88A
SynonymsAPE|GIRDIN|GIV|GRDN|HkRP1|KIAA1212|PEHO|PEHOL
Cytomap

2p16.1

Type of geneprotein-coding
DescriptiongirdinAKT-phosphorylation enhancerHook-related protein 1g alpha-interacting vesicle-associated proteingirders of actin filamentgirders of actin filaments
Modification date20180523
UniProtAcc

Q3V6T2

ContextPubMed: CCDC88A [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
CCDC88A

GO:0061024

membrane organization

15882442


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Exon skipping events across known transcript of Ensembl for CCDC88A 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 CCDC88A

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 CCDC88A

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_339216255523393:55523659:55526974:55527055:55528341:5552841355526974:55527055ENSG00000115355.11ENST00000426576.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000456975.1,ENST00000412148.1,ENST00000263630.8
exon_skip_339218255528341:55528413:55529007:55529208:55535944:5553615955529007:55529208ENSG00000115355.11ENST00000456975.1,ENST00000412148.1,ENST00000263630.8
exon_skip_339219255529007:55529208:55530204:55530288:55535944:5553615955530204:55530288ENSG00000115355.11ENST00000426576.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6
exon_skip_339221255536372:55536390:55539569:55539715:55543063:5554318755539569:55539715ENSG00000115355.11ENST00000426576.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000456975.1,ENST00000474059.1,ENST00000412148.1,ENST00000263630.8
exon_skip_339222255543063:55543250:55544341:55544485:55544699:5554488955544341:55544485ENSG00000115355.11ENST00000426576.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000456975.1,ENST00000412148.1,ENST00000263630.8
exon_skip_339223255545978:55546140:55549663:55549828:55555429:5555553255549663:55549828ENSG00000115355.11ENST00000426576.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000412148.1,ENST00000263630.8
exon_skip_339224255563816:55563954:55566599:55566784:55570783:5557092855566599:55566784ENSG00000115355.11ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000263630.8
exon_skip_339225255573310:55573469:55576653:55576735:55582714:5558288755576653:55576735ENSG00000115355.11ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000263630.8
exon_skip_339228255576653:55576735:55582714:55582887:55589443:5558958455582714:55582887ENSG00000115355.11ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000263630.8
exon_skip_339230255582847:55582887:55589443:55589584:55591085:5559116955589443:55589584ENSG00000115355.11ENST00000430086.1,ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000263630.8
exon_skip_339232255601949:55602019:55615913:55616022:55645951:5564605255615913:55616022ENSG00000115355.11ENST00000436346.1,ENST00000413716.2,ENST00000336838.6,ENST00000263630.8

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

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Exon skipping events with PSIs in GTEx for CCDC88A

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_339216255523393:55523659:55526974:55527055:55528341:5552841355526974:55527055ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000412148.1,ENST00000413716.2,ENST00000426576.1,ENST00000456975.1
exon_skip_339217255523393:55523659:55528341:55528413:55535944:5553615955528341:55528413ENSG00000115355.11ENST00000444458.1,ENST00000422883.2
exon_skip_339218255528341:55528413:55529007:55529208:55535944:5553615955529007:55529208ENSG00000115355.11ENST00000263630.8,ENST00000412148.1,ENST00000456975.1
exon_skip_339219255529007:55529208:55530204:55530288:55535944:5553615955530204:55530288ENSG00000115355.11ENST00000336838.6,ENST00000436346.1,ENST00000413716.2,ENST00000426576.1
exon_skip_339221255536372:55536390:55539569:55539715:55543063:5554318755539569:55539715ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000412148.1,ENST00000413716.2,ENST00000426576.1,ENST00000456975.1,ENST00000474059.1
exon_skip_339222255543063:55543250:55544341:55544485:55544699:5554488955544341:55544485ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000412148.1,ENST00000413716.2,ENST00000426576.1,ENST00000456975.1
exon_skip_339223255545978:55546140:55549663:55549828:55555429:5555553255549663:55549828ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000412148.1,ENST00000413716.2,ENST00000426576.1
exon_skip_339224255563816:55563954:55566599:55566784:55570783:5557092855566599:55566784ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000413716.2
exon_skip_339225255573310:55573469:55576653:55576735:55582714:5558288755576653:55576735ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000413716.2
exon_skip_339228255576653:55576735:55582714:55582887:55589443:5558958455582714:55582887ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000413716.2
exon_skip_339230255582847:55582887:55589443:55589584:55591085:5559116955589443:55589584ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000413716.2,ENST00000430086.1
exon_skip_339232255601949:55602019:55615913:55616022:55645951:5564605255615913:55616022ENSG00000115355.11ENST00000336838.6,ENST00000263630.8,ENST00000436346.1,ENST00000413716.2

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 CCDC88A

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
ENST000004363465553956955539715Frame-shift
ENST000004363465556659955566784Frame-shift
ENST000004363465557665355576735Frame-shift
ENST000004363465558271455582887Frame-shift
ENST000004363465561591355616022Frame-shift
ENST000004363465552697455527055In-frame
ENST000004363465553020455530288In-frame
ENST000004363465554434155544485In-frame
ENST000004363465554966355549828In-frame
ENST000004363465558944355589584In-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
ENST000004363465553956955539715Frame-shift
ENST000004363465556659955566784Frame-shift
ENST000004363465557665355576735Frame-shift
ENST000004363465558271455582887Frame-shift
ENST000004363465561591355616022Frame-shift
ENST000004363465552697455527055In-frame
ENST000004363465553020455530288In-frame
ENST000004363465554434155544485In-frame
ENST000004363465554966355549828In-frame
ENST000004363465558944355589584In-frame

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Infer the effects of exon skipping event on protein functional features for CCDC88A

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
ENST0000043634698281871555894435558958413291469162209
ENST00000436346982818715554966355549828384040049991054
ENST000004363469828187155544341555444854445458812011248
ENST000004363469828187155530204555302885230531314621490
ENST000004363469828187155526974555270555587566715811608

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
ENST0000043634698281871555894435558958413291469162209
ENST00000436346982818715554966355549828384040049991054
ENST000004363469828187155544341555444854445458812011248
ENST000004363469828187155530204555302885230531314621490
ENST000004363469828187155526974555270555587566715811608

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 CCDC88A

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_339219
55530205555302885553027455530274Frame_Shift_DelT-p.R1468fs
LIHCTCGA-DD-A3A0-01exon_skip_339222
55544342555444855554439355544393Frame_Shift_DelT-p.N1232fs
LIHCTCGA-G3-A3CJ-01exon_skip_339222
55544342555444855554439355544393Frame_Shift_DelT-p.N1232fs
LIHCTCGA-DD-A3A0-01exon_skip_339222
55544342555444855554439955544399Frame_Shift_DelT-p.N1230fs
LIHCTCGA-G3-A3CJ-01exon_skip_339222
55544342555444855554439955544399Frame_Shift_DelT-p.N1230fs
LIHCTCGA-DD-A3A0-01exon_skip_339222
55544342555444855554441255544412Frame_Shift_DelT-p.M1226fs
STADTCGA-BR-4201-01exon_skip_339222
55544342555444855554443655544436Frame_Shift_DelT-p.M1217fs
STADTCGA-BR-8363-01exon_skip_339222
55544342555444855554443655544436Frame_Shift_DelT-p.M1217fs
STADTCGA-BR-8363-01exon_skip_339222
55544342555444855554443655544436Frame_Shift_DelT-p.M1218fs
LIHCTCGA-DD-A1EG-01exon_skip_339223
55549664555498285554976455549764Frame_Shift_DelG-p.P1022fs
LIHCTCGA-DD-A3A0-0155566600555667845556662455566624Frame_Shift_DelT-p.K498fs
LIHCTCGA-DD-A39Y-0155566600555667845556663255566632Frame_Shift_DelT-p.M496fs
LIHCTCGA-DD-A3A0-0155566600555667845556664155566641Frame_Shift_DelT-p.I493fs
LIHCTCGA-G3-A3CJ-0155566600555667845556664155566641Frame_Shift_DelT-p.I493fs
LIHCTCGA-DD-A3A0-01exon_skip_339225
55576654555767355557668655576686Frame_Shift_DelT-p.M284fs
LIHCTCGA-G3-A3CJ-01exon_skip_339228
55582715555828875558283955582839Frame_Shift_DelG-p.H226fs
LUADTCGA-55-8302-01exon_skip_339228
55582715555828875558285155582851Frame_Shift_DelG-p.H222fs
LIHCTCGA-DD-A1EG-01exon_skip_339232
55615914556160225561598655615986Frame_Shift_DelT-p.K67fs
LIHCTCGA-G3-A3CJ-01exon_skip_339232
55615914556160225561598655615986Frame_Shift_DelT-p.K67fs
COADTCGA-A6-5665-01exon_skip_339219
55530205555302885553026055530261Frame_Shift_Ins-Ap.L1471fs
COADTCGA-G4-6628-01exon_skip_339230
55589444555895845558949555589496Frame_Shift_Ins-Tp.N192fs
ESCATCGA-VR-A8EZ-01exon_skip_339218
55529008555292085552902655529026Nonsense_MutationGAp.Q1551X
ESCATCGA-VR-A8EZ-01exon_skip_339218
55529008555292085552902655529026Nonsense_MutationGAp.Q1552*
UCECTCGA-AX-A05Z-01exon_skip_339222
55544342555444855554442455544424Nonsense_MutationCAp.E1221*
COADTCGA-A6-2676-01exon_skip_339223
55549664555498285554973255549732Nonsense_MutationGAp.R1031X
SKCMTCGA-EE-A2MS-0655566600555667845556661755566617Nonsense_MutationGAp.Q501*
BLCATCGA-E7-A6MD-01exon_skip_339225
55576654555767355557669855576698Nonsense_MutationCAp.E280*
LUADTCGA-55-8090-01exon_skip_339232
55615914556160225561593455615934Nonsense_MutationGAp.Q85*

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
BICR18_UPPER_AERODIGESTIVE_TRACT55544342555444855554442555544426Frame_Shift_DelTA-p.V1221fs
BICR18_UPPER_AERODIGESTIVE_TRACT55544342555444855554442755544428Frame_Shift_Ins-GTp.V1221fs
BICR18_UPPER_AERODIGESTIVE_TRACT55529008555292085552917055529171In_Frame_Ins-TCCp.1503_1504insG
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE55529008555292085552917055529171In_Frame_Ins-TCCp.1503_1504insG
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE55529008555292085552902855529028Missense_MutationTGp.K1551T
BICR18_UPPER_AERODIGESTIVE_TRACT55529008555292085552904055529040Missense_MutationCGp.G1547A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE55529008555292085552904055529040Missense_MutationCGp.G1547A
YD38_UPPER_AERODIGESTIVE_TRACT55529008555292085552905655529056Missense_MutationCTp.V1542I
NCIH2342_LUNG55529008555292085552920055529200Missense_MutationCTp.D1494N
NCIH2595_PLEURA55530205555302885553021455530214Missense_MutationGAp.R1488C
KYSE450_OESOPHAGUS55539570555397155553970955539709Missense_MutationTAp.S1314C
GMEL_SKIN55544342555444855554438455544384Missense_MutationGTp.T1235K
NB5_AUTONOMIC_GANGLIA55544342555444855554440655544406Missense_MutationGAp.L1228F
NCIH1666_LUNG55544342555444855554441055544410Missense_MutationCTp.M1226I
VCAP_PROSTATE55544342555444855554444555544445Missense_MutationATp.L1215M
SNU1040_LARGE_INTESTINE55549664555498285554967155549671Missense_MutationTCp.E1052G
SNU46_UPPER_AERODIGESTIVE_TRACT55549664555498285554968955549689Missense_MutationTAp.D1046V
EW11_BONE55549664555498285554971655549716Missense_MutationGAp.T1037M
LS411N_LARGE_INTESTINE55549664555498285554978255549782Missense_MutationCAp.R1015M
MFE319_ENDOMETRIUM55566600555667845556664955566649Missense_MutationGAp.A490V
KINGS1_CENTRAL_NERVOUS_SYSTEM55576654555767355557669255576692Missense_MutationCTp.E282K
NUGC2_STOMACH55582715555828875558272455582724Missense_MutationCAp.R264M
C33A_CERVIX55582715555828875558276655582766Missense_MutationGAp.S250L
CHP126_AUTONOMIC_GANGLIA55582715555828875558276655582766Missense_MutationGAp.S250L
SNU119_OVARY55582715555828875558281555582815Missense_MutationGAp.P234S
BICR18_UPPER_AERODIGESTIVE_TRACT55582715555828875558288155582881Missense_MutationTCp.I212V
HEC251_ENDOMETRIUM55589444555895845558946755589467Missense_MutationCAp.D202Y
JHUEM7_ENDOMETRIUM55615914556160225561592455615924Missense_MutationACp.F88C
MCC13_SKIN55615914556160225561601755616017Missense_MutationGAp.P57L
KYSE510_OESOPHAGUS55526975555270555552705255527052Nonsense_MutationGCp.S1583*
CHAGOK1_LUNG55544342555444855554442455544424Nonsense_MutationCAp.E1222*
JHUEM7_ENDOMETRIUM55549664555498285554972055549720Nonsense_MutationCAp.E1036*
CAL72_BONE55566600555667845556675255566752Nonsense_MutationCAp.E456*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC88A

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 CCDC88A


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC88A


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RelatedDrugs for CCDC88A

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 CCDC88A

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