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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 32118

FusionGeneSummary for RPS4Y1_CDH13

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS4Y1_CDH13
Fusion gene ID: 32118
HgeneTgene
Gene symbol

RPS4Y1

CDH13

Gene ID

6192

1012

Gene nameribosomal protein S4 Y-linked 1cadherin 13
SynonymsRPS4Y|S4CDHH|P105
Cytomap

Yp11.2

16q23.3

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4cadherin-13H-cadherin (heart)T-cadT-cadherincadherin 13, H-cadherin (heart)heart cadherin
Modification date2018052320180523
UniProtAcc

P22090

P55290

Ensembl transtripts involved in fusion geneENST00000250784, ENST00000477725, 
ENST00000566620, ENST00000268613, 
ENST00000565636, ENST00000431540, 
ENST00000428848, ENST00000567445, 
ENST00000446376, ENST00000569454, 
Fusion gene scores* DoF score4 X 4 X 2=325 X 5 X 5=125
# samples 48
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(8/125*10)=-0.643856189774725
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPS4Y1 [Title/Abstract] AND CDH13 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneCDH13

GO:0002040

sprouting angiogenesis

16873731

TgeneCDH13

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

10601632

TgeneCDH13

GO:0007162

negative regulation of cell adhesion

14729458

TgeneCDH13

GO:0008285

negative regulation of cell proliferation

10737605

TgeneCDH13

GO:0016339

calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

10601632

TgeneCDH13

GO:0030032

lamellipodium assembly

15703273

TgeneCDH13

GO:0030335

positive regulation of cell migration

14729458

TgeneCDH13

GO:0043542

endothelial cell migration

14729458

TgeneCDH13

GO:0043616

keratinocyte proliferation

15816843

TgeneCDH13

GO:0050850

positive regulation of calcium-mediated signaling

16013438

TgeneCDH13

GO:0050927

positive regulation of positive chemotaxis

16013438

TgeneCDH13

GO:0055096

low-density lipoprotein particle mediated signaling

16013438


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDGBMTCGA-06-0132-01ARPS4Y1chrY

2712298

+CDH13chr16

83158990

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shitENST00000250784ENST00000566620RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
Frame-shitENST00000250784ENST00000268613RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
Frame-shitENST00000250784ENST00000565636RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
Frame-shitENST00000250784ENST00000431540RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
5CDS-intronENST00000250784ENST00000428848RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
5CDS-intronENST00000250784ENST00000567445RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
5CDS-intronENST00000250784ENST00000446376RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
5CDS-3UTRENST00000250784ENST00000569454RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-3CDSENST00000477725ENST00000566620RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-3CDSENST00000477725ENST00000268613RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-3CDSENST00000477725ENST00000565636RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-3CDSENST00000477725ENST00000431540RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-intronENST00000477725ENST00000428848RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-intronENST00000477725ENST00000567445RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-intronENST00000477725ENST00000446376RPS4Y1chrY

2712298

+CDH13chr16

83158990

+
intron-3UTRENST00000477725ENST00000569454RPS4Y1chrY

2712298

+CDH13chr16

83158990

+

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FusionProtFeatures for RPS4Y1_CDH13


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RPS4Y1

P22090

CDH13

P55290

Cadherins are calcium-dependent cell adhesion proteins.They preferentially interact with themselves in a homophilicmanner in connecting cells; cadherins may thus contribute to thesorting of heterogeneous cell types. May act as a negativeregulator of neural cell growth. {ECO:0000269|PubMed:10737605}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for RPS4Y1_CDH13


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RPS4Y1_CDH13


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
RPS4Y1CALM1, CD81, IGSF8, ICAM1, RNF2, RPS4Y2, PRPS1, CLK1, ZNF746, CYLDCDH13MAPK6, HAX1, NUFIP1, DGUOK, DNAAF2, AURKA, CASP8, CCND1, CHEK2, HMMR, PTPN1, RAD51, SEC14L1, AGPAT5, INSIG1, DSTYK, RRAGB, ERMP1, VMP1, UQCC1, TUBB3, CHPT1, TUBB8, GHITM, ARF5, PIGU, TMX4, RPL23, MTNR1B


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for RPS4Y1_CDH13


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RPS4Y1_CDH13


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCDH13C0001973Alcoholic Intoxication, Chronic3PSYGENET
TgeneCDH13C0033578Prostatic Neoplasms2CTD_human
TgeneCDH13C2239176Liver carcinoma2CTD_human
TgeneCDH13C0004763Barrett Esophagus1CTD_human
TgeneCDH13C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneCDH13C0011570Mental Depression1PSYGENET
TgeneCDH13C0011581Depressive disorder1PSYGENET
TgeneCDH13C0014859Esophageal Neoplasms1CTD_human
TgeneCDH13C0024121Lung Neoplasms1CTD_human
TgeneCDH13C0236733Amphetamine-Related Disorders1CTD_human
TgeneCDH13C0236969Substance-Related Disorders1CTD_human