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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 YIPF3

check button Gene summary
Gene informationGene symbol

YIPF3

Gene ID

25844

Gene nameYip1 domain family member 3
SynonymsC6orf109|FinGER3|KLIP1|dJ337H4.3
Cytomap

6p21.1

Type of geneprotein-coding
Descriptionprotein YIPF3killer lineage protein 1natural killer cell-specific antigen KLIP1
Modification date20180519
UniProtAcc

Q9GZM5

ContextPubMed: YIPF3 [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

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Exon skipping events across known transcript of Ensembl for YIPF3 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 YIPF3

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 YIPF3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459721643479957:43480053:43480177:43480301:43480498:4348061243480177:43480301ENSG00000137207.7ENST00000506469.1,ENST00000503147.1,ENST00000510102.1,ENST00000490447.2,ENST00000372422.2
exon_skip_459729643480272:43480301:43480498:43480612:43480806:4348083643480498:43480612ENSG00000137207.7ENST00000512713.1,ENST00000514627.1,ENST00000506469.1,ENST00000510102.1,ENST00000503972.1,ENST00000490447.2,ENST00000372422.2
exon_skip_459732643480565:43480612:43480806:43480836:43481096:4348117943480806:43480836ENSG00000137207.7ENST00000503972.1
exon_skip_459733643480565:43480612:43480806:43480938:43481096:4348117943480806:43480938ENSG00000137207.7ENST00000506469.1,ENST00000510102.1,ENST00000416380.2,ENST00000490447.2,ENST00000455768.2,ENST00000372422.2,ENST00000372417.1
exon_skip_459736643480565:43480612:43480806:43481189:43481325:4348137143480806:43481189ENSG00000137207.7ENST00000514627.1
exon_skip_459742643480879:43480938:43481096:43481189:43481325:4348137143481096:43481189ENSG00000137207.7ENST00000506469.1,ENST00000510102.1,ENST00000500090.2,ENST00000416380.2,ENST00000490447.2,ENST00000455768.2,ENST00000372422.2,ENST00000372417.1
exon_skip_459743643481096:43481189:43481325:43481371:43483332:4348338543481325:43481371ENSG00000137207.7ENST00000488966.1,ENST00000506469.1,ENST00000416380.2,ENST00000503972.1,ENST00000490447.2,ENST00000455768.2,ENST00000372422.2
exon_skip_459744643481096:43481189:43481325:43481371:43483343:4348343943481325:43481371ENSG00000137207.7ENST00000510102.1
exon_skip_459745643481333:43481371:43482930:43483044:43483332:4348338543482930:43483044ENSG00000137207.7ENST00000500090.2
exon_skip_459746643481333:43481371:43483332:43483439:43483626:4348378443483332:43483439ENSG00000137207.7ENST00000511831.1,ENST00000506469.1,ENST00000416380.2,ENST00000503972.1,ENST00000490447.2,ENST00000455768.2,ENST00000502714.1,ENST00000372422.2
exon_skip_459747643481333:43481371:43483343:43483439:43483626:4348378443483343:43483439ENSG00000137207.7ENST00000510102.1
exon_skip_459748643483343:43483439:43483626:43483784:43484464:4348465743483626:43483784ENSG00000137207.7ENST00000455768.2
exon_skip_459750643483343:43483439:43483626:43483833:43484464:4348465743483626:43483833ENSG00000137207.7ENST00000503972.1,ENST00000460903.2
exon_skip_459751643483343:43483439:43483626:43483851:43484464:4348465743483626:43483851ENSG00000137207.7ENST00000506469.1
exon_skip_459753643483343:43483439:43483626:43483925:43484464:4348465743483626:43483925ENSG00000137207.7ENST00000510102.1,ENST00000416380.2
exon_skip_459754643483343:43483439:43483626:43483928:43484464:4348465743483626:43483928ENSG00000137207.7ENST00000490447.2

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

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Exon skipping events with PSIs in GTEx for YIPF3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_459721643479957:43480053:43480177:43480301:43480498:4348061243480177:43480301ENSG00000137207.7ENST00000372422.2,ENST00000510102.1,ENST00000506469.1,ENST00000490447.2,ENST00000503147.1
exon_skip_459729643480272:43480301:43480498:43480612:43480806:4348083643480498:43480612ENSG00000137207.7ENST00000372422.2,ENST00000510102.1,ENST00000506469.1,ENST00000490447.2,ENST00000503972.1,ENST00000514627.1,ENST00000512713.1
exon_skip_459732643480565:43480612:43480806:43480836:43481096:4348117943480806:43480836ENSG00000137207.7ENST00000503972.1
exon_skip_459733643480565:43480612:43480806:43480938:43481096:4348117943480806:43480938ENSG00000137207.7ENST00000372422.2,ENST00000510102.1,ENST00000506469.1,ENST00000490447.2,ENST00000455768.2,ENST00000416380.2,ENST00000372417.1
exon_skip_459736643480565:43480612:43480806:43481189:43481325:4348137143480806:43481189ENSG00000137207.7ENST00000514627.1
exon_skip_459742643480879:43480938:43481096:43481189:43481325:4348137143481096:43481189ENSG00000137207.7ENST00000372422.2,ENST00000510102.1,ENST00000506469.1,ENST00000490447.2,ENST00000455768.2,ENST00000416380.2,ENST00000372417.1,ENST00000500090.2
exon_skip_459743643481096:43481189:43481325:43481371:43483332:4348338543481325:43481371ENSG00000137207.7ENST00000372422.2,ENST00000506469.1,ENST00000490447.2,ENST00000503972.1,ENST00000455768.2,ENST00000416380.2,ENST00000488966.1
exon_skip_459744643481096:43481189:43481325:43481371:43483343:4348343943481325:43481371ENSG00000137207.7ENST00000510102.1
exon_skip_459745643481333:43481371:43482930:43483044:43483332:4348338543482930:43483044ENSG00000137207.7ENST00000500090.2
exon_skip_459746643481333:43481371:43483332:43483439:43483626:4348378443483332:43483439ENSG00000137207.7ENST00000372422.2,ENST00000506469.1,ENST00000490447.2,ENST00000503972.1,ENST00000455768.2,ENST00000416380.2,ENST00000502714.1,ENST00000511831.1
exon_skip_459747643481333:43481371:43483343:43483439:43483626:4348378443483343:43483439ENSG00000137207.7ENST00000510102.1
exon_skip_459748643483343:43483439:43483626:43483784:43484464:4348465743483626:43483784ENSG00000137207.7ENST00000455768.2
exon_skip_459750643483343:43483439:43483626:43483833:43484464:4348465743483626:43483833ENSG00000137207.7ENST00000503972.1,ENST00000460903.2
exon_skip_459751643483343:43483439:43483626:43483851:43484464:4348465743483626:43483851ENSG00000137207.7ENST00000506469.1
exon_skip_459753643483343:43483439:43483626:43483925:43484464:4348465743483626:43483925ENSG00000137207.7ENST00000510102.1,ENST00000416380.2
exon_skip_459754643483343:43483439:43483626:43483928:43484464:4348465743483626:43483928ENSG00000137207.7ENST00000490447.2

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 YIPF3

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
ENST000003724224348017743480301Frame-shift
ENST000003724224348132543481371Frame-shift
ENST000003724224348333243483439Frame-shift
ENST000003724224348049843480612In-frame
ENST000003724224348080643480938In-frame
ENST000003724224348109643481189In-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
ENST000003724224348017743480301Frame-shift
ENST000003724224348132543481371Frame-shift
ENST000003724224348333243483439Frame-shift
ENST000003724224348049843480612In-frame
ENST000003724224348080643480938In-frame
ENST000003724224348109643481189In-frame

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Infer the effects of exon skipping event on protein functional features for YIPF3

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
ENST0000037242215933504348109643481189625717147178
ENST0000037242215933504348080643480938718849178222
ENST0000037242215933504348049843480612850963222260

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
ENST0000037242215933504348109643481189625717147178
ENST0000037242215933504348080643480938718849178222
ENST0000037242215933504348049843480612850963222260

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
Q9GZM51471782350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5147178161161Sequence conflictNote=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM51471782148Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:27999994;Dbxref=PMID:27999994
Q9GZM5147178170187Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5147178149169TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM51782222350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5178222170187Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5178222209214Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5178222188208TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM5178222215237TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM52222602350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5222260238240Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5222260215237TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM5222260241263TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255


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
Q9GZM51471782350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5147178161161Sequence conflictNote=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM51471782148Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:27999994;Dbxref=PMID:27999994
Q9GZM5147178170187Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5147178149169TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM51782222350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5178222170187Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5178222209214Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5178222188208TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM5178222215237TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM52222602350ChainID=PRO_0000244446;Note=Protein YIPF3
Q9GZM5222260238240Topological domainNote=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9GZM5222260215237TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9GZM5222260241263TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255


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SNVs in the skipped exons for YIPF3

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
KIRPTCGA-A4-A5XZ-01exon_skip_459746
exon_skip_459747
43483333434834394348337943483379Frame_Shift_DelT-p.I117fs
KIRPTCGA-A4-A5XZ-01exon_skip_459746
exon_skip_459747
43483344434834394348337943483379Frame_Shift_DelT-p.I117fs
LIHCTCGA-DD-A3A0-01exon_skip_459746
exon_skip_459747
43483333434834394348340643483406Frame_Shift_DelC-p.A108fs
LIHCTCGA-DD-A3A0-01exon_skip_459746
exon_skip_459747
43483344434834394348340643483406Frame_Shift_DelC-p.A108fs
HNSCTCGA-CV-A6K2-01exon_skip_459748
43483627434837844348362943483629Nonsense_MutationGAp.Q96*
HNSCTCGA-CV-A6K2-01exon_skip_459750
43483627434838334348362943483629Nonsense_MutationGAp.Q96*
HNSCTCGA-CV-A6K2-01exon_skip_459751
43483627434838514348362943483629Nonsense_MutationGAp.Q96*
HNSCTCGA-CV-A6K2-01exon_skip_459753
43483627434839254348362943483629Nonsense_MutationGAp.Q96*
HNSCTCGA-CV-A6K2-01exon_skip_459754
43483627434839284348362943483629Nonsense_MutationGAp.Q96*
BLCATCGA-DK-AA6U-01exon_skip_459750
43483627434838334348380643483806Nonsense_MutationCAp.E37*
BLCATCGA-DK-AA6U-01exon_skip_459751
43483627434838514348380643483806Nonsense_MutationCAp.E37*
BLCATCGA-DK-AA6U-01exon_skip_459753
43483627434839254348380643483806Nonsense_MutationCAp.E37*
BLCATCGA-DK-AA6U-01exon_skip_459754
43483627434839284348380643483806Nonsense_MutationCAp.E37*
CESCTCGA-IR-A3LH-01exon_skip_459746
exon_skip_459747
43483333434834394348344043483440Splice_SiteCTe3-1
CESCTCGA-IR-A3LH-01exon_skip_459746
exon_skip_459747
43483344434834394348344043483440Splice_SiteCTe3-1

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
HT29_LARGE_INTESTINE43480178434803014348025643480256Missense_MutationGCp.L276V
HEC59_ENDOMETRIUM43480178434803014348029543480295Missense_MutationCTp.V263M
C75_LARGE_INTESTINE43480499434806124348056643480566Missense_MutationTCp.N238S
SNU1040_LARGE_INTESTINE43480499434806124348059043480590Missense_MutationCTp.C230Y
CFPAC1_PANCREAS43480807434809384348083343480833Missense_MutationTAp.T214S
CFPAC1_PANCREAS43480807434808364348083343480833Missense_MutationTAp.T214S
CFPAC1_PANCREAS43480807434811894348083343480833Missense_MutationTAp.T214S
SNGM_ENDOMETRIUM43480807434809384348086043480860Missense_MutationGTp.L205I
SNGM_ENDOMETRIUM43480807434811894348086043480860Missense_MutationGTp.L205I
OE33_OESOPHAGUS43481097434811894348111343481113Missense_MutationGAp.T173M
OE33_OESOPHAGUS43480807434811894348111343481113Missense_MutationGAp.T173M
QIMRWIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE43481097434811894348111443481114Missense_MutationTCp.T173A
QIMRWIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE43480807434811894348111443481114Missense_MutationTCp.T173A
HSC1_SKIN43481097434811894348116443481164Missense_MutationGAp.P156L
HSC1_SKIN43480807434811894348116443481164Missense_MutationGAp.P156L
HEC59_ENDOMETRIUM43483627434839284348370943483709Missense_MutationGAp.A69V
HEC59_ENDOMETRIUM43483627434839254348370943483709Missense_MutationGAp.A69V
HEC59_ENDOMETRIUM43483627434838514348370943483709Missense_MutationGAp.A69V
HEC59_ENDOMETRIUM43483627434838334348370943483709Missense_MutationGAp.A69V
HEC59_ENDOMETRIUM43483627434837844348370943483709Missense_MutationGAp.A69V
769P_KIDNEY43480807434809384348093843480938Splice_SiteGAp.R179W
769P_KIDNEY43480807434811894348093843480938Splice_SiteGAp.R179W

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YIPF3

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 YIPF3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for YIPF3


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RelatedDrugs for YIPF3

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 YIPF3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
YIPF3C0007134Renal Cell Carcinoma1CTD_human