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Fusion gene ID: 32118 |
FusionGeneSummary for RPS4Y1_CDH13 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RPS4Y1_CDH13 | Fusion gene ID: 32118 | Hgene | Tgene | Gene symbol | RPS4Y1 | CDH13 | Gene ID | 6192 | 1012 |
| Gene name | ribosomal protein S4 Y-linked 1 | cadherin 13 | |
| Synonyms | RPS4Y|S4 | CDHH|P105 | |
| Cytomap | Yp11.2 | 16q23.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | 40S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4 | cadherin-13H-cadherin (heart)T-cadT-cadherincadherin 13, H-cadherin (heart)heart cadherin | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P22090 | P55290 | |
| Ensembl transtripts involved in fusion gene | ENST00000250784, ENST00000477725, | ENST00000566620, ENST00000268613, ENST00000565636, ENST00000431540, ENST00000428848, ENST00000567445, ENST00000446376, ENST00000569454, | |
| Fusion gene scores | * DoF score | 4 X 4 X 2=32 | 5 X 5 X 5=125 |
| # samples | 4 | 8 | |
| ** MAII score | log2(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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Tgene | CDH13 | GO:0002040 | sprouting angiogenesis | 16873731 |
| Tgene | CDH13 | GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | 10601632 |
| Tgene | CDH13 | GO:0007162 | negative regulation of cell adhesion | 14729458 |
| Tgene | CDH13 | GO:0008285 | negative regulation of cell proliferation | 10737605 |
| Tgene | CDH13 | GO:0016339 | calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules | 10601632 |
| Tgene | CDH13 | GO:0030032 | lamellipodium assembly | 15703273 |
| Tgene | CDH13 | GO:0030335 | positive regulation of cell migration | 14729458 |
| Tgene | CDH13 | GO:0043542 | endothelial cell migration | 14729458 |
| Tgene | CDH13 | GO:0043616 | keratinocyte proliferation | 15816843 |
| Tgene | CDH13 | GO:0050850 | positive regulation of calcium-mediated signaling | 16013438 |
| Tgene | CDH13 | GO:0050927 | positive regulation of positive chemotaxis | 16013438 |
| Tgene | CDH13 | GO:0055096 | low-density lipoprotein particle mediated signaling | 16013438 |
| 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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | LD | GBM | TCGA-06-0132-01A | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| Frame-shift | ENST00000250784 | ENST00000566620 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| Frame-shift | ENST00000250784 | ENST00000268613 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| Frame-shift | ENST00000250784 | ENST00000565636 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| Frame-shift | ENST00000250784 | ENST00000431540 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| 5CDS-intron | ENST00000250784 | ENST00000428848 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| 5CDS-intron | ENST00000250784 | ENST00000567445 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| 5CDS-intron | ENST00000250784 | ENST00000446376 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| 5CDS-3UTR | ENST00000250784 | ENST00000569454 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-3CDS | ENST00000477725 | ENST00000566620 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-3CDS | ENST00000477725 | ENST00000268613 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-3CDS | ENST00000477725 | ENST00000565636 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-3CDS | ENST00000477725 | ENST00000431540 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-intron | ENST00000477725 | ENST00000428848 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-intron | ENST00000477725 | ENST00000567445 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-intron | ENST00000477725 | ENST00000446376 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
| intron-3UTR | ENST00000477725 | ENST00000569454 | RPS4Y1 | chrY | 2712298 | + | CDH13 | chr16 | 83158990 | + |
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FusionProtFeatures for RPS4Y1_CDH13 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RPS4Y1 | CDH13 |
| 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}. |
| Retention 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 . * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for RPS4Y1_CDH13 |
| 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 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| RPS4Y1 | CALM1, CD81, IGSF8, ICAM1, RNF2, RPS4Y2, PRPS1, CLK1, ZNF746, CYLD | CDH13 | MAPK6, 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 |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for RPS4Y1_CDH13 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for RPS4Y1_CDH13 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | CDH13 | C0001973 | Alcoholic Intoxication, Chronic | 3 | PSYGENET |
| Tgene | CDH13 | C0033578 | Prostatic Neoplasms | 2 | CTD_human |
| Tgene | CDH13 | C2239176 | Liver carcinoma | 2 | CTD_human |
| Tgene | CDH13 | C0004763 | Barrett Esophagus | 1 | CTD_human |
| Tgene | CDH13 | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |
| Tgene | CDH13 | C0011570 | Mental Depression | 1 | PSYGENET |
| Tgene | CDH13 | C0011581 | Depressive disorder | 1 | PSYGENET |
| Tgene | CDH13 | C0014859 | Esophageal Neoplasms | 1 | CTD_human |
| Tgene | CDH13 | C0024121 | Lung Neoplasms | 1 | CTD_human |
| Tgene | CDH13 | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |
| Tgene | CDH13 | C0236969 | Substance-Related Disorders | 1 | CTD_human |
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