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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:RAB40B-YBX2 (FusionGDB2 ID:70960) |
Fusion Gene Summary for RAB40B-YBX2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RAB40B-YBX2 | Fusion gene ID: 70960 | Hgene | Tgene | Gene symbol | RAB40B | YBX2 | Gene ID | 10966 | 51087 |
| Gene name | RAB40B, member RAS oncogene family | Y-box binding protein 2 | |
| Synonyms | RAR|SEC4L | CONTRIN|CSDA3|DBPC|MSY2 | |
| Cytomap | 17q25.3 | 17p13.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | ras-related protein Rab-40BGTP-binding protein homologous to Saccharomyces cerevisiae SEC4SOCS box-containing protein RARprotein Rar | Y-box-binding protein 2DNA-binding protein Cepididymis secretory sperm binding proteingerm cell specific Y-box binding protein | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | . | . | |
| Ensembl transtripts involved in fusion gene | ENST00000571995, ENST00000571880, ENST00000269347, ENST00000538809, | ENST00000007699, ENST00000570627, | |
| Fusion gene scores | * DoF score | 5 X 3 X 4=60 | 6 X 4 X 5=120 |
| # samples | 5 | 6 | |
| ** MAII score | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RAB40B [Title/Abstract] AND YBX2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | RAB40B(80656331)-YBX2(7193854), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 |
| Fusion gene breakpoints across RAB40B (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across YBX2 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | LIHC | TCGA-ZS-A9CD-01A | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| ChimerDB4 | LIHC | TCGA-ZS-A9CD-01A | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
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Fusion Gene ORF analysis for RAB40B-YBX2 |
| 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 |
| In-frame | ENST00000571995 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| 5CDS-5UTR | ENST00000571995 | ENST00000570627 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| intron-3CDS | ENST00000571880 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| intron-5UTR | ENST00000571880 | ENST00000570627 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| 5UTR-3CDS | ENST00000269347 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| 5UTR-5UTR | ENST00000269347 | ENST00000570627 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| In-frame | ENST00000538809 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| 5CDS-5UTR | ENST00000538809 | ENST00000570627 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000571995 | RAB40B | chr17 | 80656331 | - | ENST00000007699 | YBX2 | chr17 | 7193854 | - | 1341 | 274 | 238 | 909 | 223 |
| ENST00000538809 | RAB40B | chr17 | 80656331 | - | ENST00000007699 | YBX2 | chr17 | 7193854 | - | 1275 | 208 | 172 | 843 | 223 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000571995 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - | 0.5568494 | 0.4431506 |
| ENST00000538809 | ENST00000007699 | RAB40B | chr17 | 80656331 | - | YBX2 | chr17 | 7193854 | - | 0.52554005 | 0.47446 |
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Fusion Genomic Features for RAB40B-YBX2 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for RAB40B-YBX2 |
| Go to FGviewer for the breakpoints of chr17:80656331-chr17:7193854 - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | . |
| FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. | FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. |
| 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 |
| Hgene | RAB40B | chr17:80656331 | chr17:7193854 | ENST00000571995 | - | 1 | 6 | 21_28 | 47.333333333333336 | 279.0 | Nucleotide binding | GTP |
| Tgene | YBX2 | chr17:80656331 | chr17:7193854 | ENST00000007699 | 3 | 9 | 185_352 | 153.0 | 392.6666666666667 | Compositional bias | Note=Pro-rich | |
| Tgene | YBX2 | chr17:80656331 | chr17:7193854 | ENST00000007699 | 3 | 9 | 217_364 | 153.0 | 392.6666666666667 | Region | Note=Required for mRNA-binding |
| - 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 |
| Hgene | RAB40B | chr17:80656331 | chr17:7193854 | ENST00000571995 | - | 1 | 6 | 175_228 | 47.333333333333336 | 279.0 | Domain | SOCS box |
| Hgene | RAB40B | chr17:80656331 | chr17:7193854 | ENST00000571995 | - | 1 | 6 | 126_129 | 47.333333333333336 | 279.0 | Nucleotide binding | GTP |
| Hgene | RAB40B | chr17:80656331 | chr17:7193854 | ENST00000571995 | - | 1 | 6 | 69_73 | 47.333333333333336 | 279.0 | Nucleotide binding | GTP |
| Tgene | YBX2 | chr17:80656331 | chr17:7193854 | ENST00000007699 | 3 | 9 | 35_67 | 153.0 | 392.6666666666667 | Compositional bias | Note=Gly-rich | |
| Tgene | YBX2 | chr17:80656331 | chr17:7193854 | ENST00000007699 | 3 | 9 | 93_163 | 153.0 | 392.6666666666667 | Domain | Note=CSD | |
| Tgene | YBX2 | chr17:80656331 | chr17:7193854 | ENST00000007699 | 3 | 9 | 87_169 | 153.0 | 392.6666666666667 | Region | Required for cytoplasmic retention |
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Fusion Gene Sequence for RAB40B-YBX2 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >In-frame_ENST00000571995_ENST00000007699_TCGA-ZS-A9CD-01A_RAB40B_chr17_80656331_-_YBX2_chr17_7193854_length(transcript)=1341nt_BP=274nt AGCGCTGGGCGGCGGGGCGGGGCCGGAGGCGAGCAAGGACTCGGGGCCCGCGCGGCGCCTCTCGGGGCCGGGCCGCCGCCTCTGCGCTCA GCCCCGCAGGCCGGGCATGGGTGGGGGCGCCGGGCCGTCACGATGAGCGCCCTGGGCAGCCCGGTCCGGGCCTACGACTTTCTGCTCAAG TTCCTGCTGGTGGGCGACAGCGACGTGGGCAAGGGCGAGATCCTGGCGAGCCTGCAGGATGGCGCGGCCGAGTCCCCGTACGGCCACCCG GCGGGGCGCAGAAGCCACTAATGTAACTGGGCCTGGGGGAGTACCCGTGAAGGGCAGCCGTTATGCCCCCAACCGACGTAAGTCCCGCCG ATTCATCCCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGAGATCCCCTCGGCGGGGACAGGACCTGGCAGTAAAGGGGAGCG GGCTGAAGACTCTGGGCAACGGCCCCGACGATGGTGCCCCCCACCCTTCTTCTACCGACGGCGGTTTGTGCGAGGCCCCCGGCCTCCCAA CCAGCAGCAGCCTATAGAGGGCACTGACAGGGTAGAACCCAAAGAGACAGCCCCATTGGAGGGGCACCAACAGCAGGGAGATGAGCGAGT CCCCCCGCCCAGATTCCGGCCCAGGTACCGAAGGCCTTTCCGCCCCAGGCCACGCCAGCAGCCTACCACAGAAGGTGGGGATGGTGAGAC CAAGCCCAGCCAAGGTCCCGCTGATGGTTCCCGGCCTGAGCCCCAGCGCCCACGAAACCGCCCCTACTTCCAGCGGAGACGGCAGCAGGC CCCTGGCCCCCAGCAGGCCCCTGGCCCCCGGCAGCCCGCAGCCCCTGAGACCTCAGCCCCTGTCAACAGTGGGGACCCCACCACCACCAT CCTGGAGTGATTCCAACTCAACTCAGAGGACACCCAGAGCTGCCATCTGGTATCTGCCAGTTTTTCCAAATGACCTGTACCCTACCCAGT ACCCTGCTCCCCCTTTCCCATAATTCATGACATCAAAACACCAGCTTTTCACCTTTTCCTTGAGACTCAGGAGGACCAAAGCAGCAGCCT TTTGCTTTTTCTTTTTTCTTCCCTCCCCTTATCAAGGGTTGAAGGAAGGGAGCCATCCTTACTGTTCAGAGACAGCAACTCCCTCCCGTA ACTCAGGCTGAGAAGGAACCAGCCAGCTCTTACCTCCTCCTGGTTGCTTTTCTTGCCCCCACCCCAAGTTTATTTTTGTTTTCCCCCGGC >In-frame_ENST00000571995_ENST00000007699_TCGA-ZS-A9CD-01A_RAB40B_chr17_80656331_-_YBX2_chr17_7193854_length(amino acids)=223AA_start in transcript=238_stop in transcript=909 MARPSPRTATRRGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPRPPSVAPPPMVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYR RRFVRGPRPPNQQQPIEGTDRVEPKETAPLEGHQQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQGPADGSRPEPQRPRN -------------------------------------------------------------- >In-frame_ENST00000538809_ENST00000007699_TCGA-ZS-A9CD-01A_RAB40B_chr17_80656331_-_YBX2_chr17_7193854_length(transcript)=1275nt_BP=208nt GCCGGGCCGCCGCCTCTGCGCTCAGCCCCGCAGGCCGGGCATGGGTGGGGGCGCCGGGCCGTCACGATGAGCGCCCTGGGCAGCCCGGTC CGGGCCTACGACTTTCTGCTCAAGTTCCTGCTGGTGGGCGACAGCGACGTGGGCAAGGGCGAGATCCTGGCGAGCCTGCAGGATGGCGCG GCCGAGTCCCCGTACGGCCACCCGGCGGGGCGCAGAAGCCACTAATGTAACTGGGCCTGGGGGAGTACCCGTGAAGGGCAGCCGTTATGC CCCCAACCGACGTAAGTCCCGCCGATTCATCCCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGAGATCCCCTCGGCGGGGAC AGGACCTGGCAGTAAAGGGGAGCGGGCTGAAGACTCTGGGCAACGGCCCCGACGATGGTGCCCCCCACCCTTCTTCTACCGACGGCGGTT TGTGCGAGGCCCCCGGCCTCCCAACCAGCAGCAGCCTATAGAGGGCACTGACAGGGTAGAACCCAAAGAGACAGCCCCATTGGAGGGGCA CCAACAGCAGGGAGATGAGCGAGTCCCCCCGCCCAGATTCCGGCCCAGGTACCGAAGGCCTTTCCGCCCCAGGCCACGCCAGCAGCCTAC CACAGAAGGTGGGGATGGTGAGACCAAGCCCAGCCAAGGTCCCGCTGATGGTTCCCGGCCTGAGCCCCAGCGCCCACGAAACCGCCCCTA CTTCCAGCGGAGACGGCAGCAGGCCCCTGGCCCCCAGCAGGCCCCTGGCCCCCGGCAGCCCGCAGCCCCTGAGACCTCAGCCCCTGTCAA CAGTGGGGACCCCACCACCACCATCCTGGAGTGATTCCAACTCAACTCAGAGGACACCCAGAGCTGCCATCTGGTATCTGCCAGTTTTTC CAAATGACCTGTACCCTACCCAGTACCCTGCTCCCCCTTTCCCATAATTCATGACATCAAAACACCAGCTTTTCACCTTTTCCTTGAGAC TCAGGAGGACCAAAGCAGCAGCCTTTTGCTTTTTCTTTTTTCTTCCCTCCCCTTATCAAGGGTTGAAGGAAGGGAGCCATCCTTACTGTT CAGAGACAGCAACTCCCTCCCGTAACTCAGGCTGAGAAGGAACCAGCCAGCTCTTACCTCCTCCTGGTTGCTTTTCTTGCCCCCACCCCA AGTTTATTTTTGTTTTCCCCCGGCCCCCTACCTCTGAAGCCATTTTATGATCTGTCATGTGCCACCTGAGCCTCCAGTAAAAACAAAAAC >In-frame_ENST00000538809_ENST00000007699_TCGA-ZS-A9CD-01A_RAB40B_chr17_80656331_-_YBX2_chr17_7193854_length(amino acids)=223AA_start in transcript=172_stop in transcript=843 MARPSPRTATRRGAEATNVTGPGGVPVKGSRYAPNRRKSRRFIPRPPSVAPPPMVAEIPSAGTGPGSKGERAEDSGQRPRRWCPPPFFYR RRFVRGPRPPNQQQPIEGTDRVEPKETAPLEGHQQQGDERVPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQGPADGSRPEPQRPRN -------------------------------------------------------------- |
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Fusion Gene PPI Analysis for RAB40B-YBX2 |
| 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 |
| - 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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Related Drugs for RAB40B-YBX2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for RAB40B-YBX2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RAB40B | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
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