|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 41331 |
FusionGeneSummary for VAMP4_MYRFL |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VAMP4_MYRFL | Fusion gene ID: 41331 | Hgene | Tgene | Gene symbol | VAMP4 | MYRFL | Gene ID | 8674 | 196446 |
| Gene name | vesicle associated membrane protein 4 | myelin regulatory factor like | |
| Synonyms | VAMP-4|VAMP24 | C12orf15|C12orf28|bcm1377 | |
| Cytomap | 1q24.3 | 12q15 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vesicle-associated membrane protein 4VAMP4/TAF3 fusion | myelin regulatory factor-like protein | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | O75379 | Q96LU7 | |
| Ensembl transtripts involved in fusion gene | ENST00000236192, ENST00000415773, ENST00000367740, ENST00000482519, | ENST00000552032, ENST00000547771, ENST00000299350, ENST00000535034, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 24 X 10 X 4=960 |
| # samples | 1 | 21 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(21/960*10)=-2.1926450779424 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VAMP4 [Title/Abstract] AND MYRFL [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 |
| Hgene | VAMP4 | GO:0035493 | SNARE complex assembly | 21151919 |
| 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 | SARC | TCGA-FX-A2QS-01A | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| * 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 | ENST00000236192 | ENST00000552032 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| Frame-shift | ENST00000236192 | ENST00000547771 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000236192 | ENST00000299350 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000236192 | ENST00000535034 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| In-frame | ENST00000415773 | ENST00000552032 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| In-frame | ENST00000415773 | ENST00000547771 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000415773 | ENST00000299350 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000415773 | ENST00000535034 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| Frame-shift | ENST00000367740 | ENST00000552032 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| Frame-shift | ENST00000367740 | ENST00000547771 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000367740 | ENST00000299350 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5CDS-intron | ENST00000367740 | ENST00000535034 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5UTR-3CDS | ENST00000482519 | ENST00000552032 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5UTR-3CDS | ENST00000482519 | ENST00000547771 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5UTR-intron | ENST00000482519 | ENST00000299350 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
| 5UTR-intron | ENST00000482519 | ENST00000535034 | VAMP4 | chr1 | 171707489 | - | MYRFL | chr12 | 70320351 | + |
Top |
FusionProtFeatures for VAMP4_MYRFL |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VAMP4 | MYRFL |
| Involved in the pathway that functions to remove aninhibitor (probably synaptotagmin-4) of calcium-triggeredexocytosis during the maturation of secretory granules. May be amarker for this sorting pathway that is critical for remodelingthe secretory response of granule. |
| 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 |
Top |
FusionGeneSequence for VAMP4_MYRFL |
| 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. |
| >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000552032_chr12_70320351_+_399aa MPPKFKRHLNDDDVTGSVKSERDQIFMENVGAVKQLCKLTNNLEERIEELEIWNRKLARLKRLSSWKSSASEASTISKSSRAVSASSPRR AVHKKNNKVYFSGKRQACPNWVFQTLVITLIAVMAFCALTIVALYILSLKDQDRRVPNLPPSNITSSQEPALLPTASSSAPNTSLVTTPA SLQVPEITFCEILPCQETYCCPIRGMKEVSSSPVQRQSEEKEFHQRRWSEDKSKSVLARNALSGPDWESDWIDTTISSIQIMEIQQIIDH QYCIQSLQCGSGNYNYNIPVNKHTPTNVKFSLEINTTEPLIVFQCKFTLGNICFHSKRGTKGLESHREISQEMTQGYQHIWSLPVAPFSD >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000547771_chr12_70320351_+_387aa MPPKFKRHLNDDDVTGSVKSERDQIFMENVGAVKQLCKLTNNLEERIEELEIWNRKLARLKRLSSWKSSASEASTISKSSRAVSASSPRR AVHKKNNKVYFSGKRQACPNWVFQTLVITLIAVMAFCLKDQDRRVPNLPPSNITSSQEPALLPTASSSAPNTSLVTTPASLQVPEITFCE ILPCQETYCCPIRGMKEVSSSPVQRQSEEKEFHQRRWSDKSKSVLARNALSGPDWESDWIDTTISSIQIMEIQQIIDHQYCIQSLQCGSG NYNYNIPVNKHTPTNVKFSLEINTTEPLIVFQCKFTLGNICFHSKRGTKGLESHREISQEMTQGYQHIWSLPVAPFSDSMFHFRVAAPDL |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000552032_chr12_70320351_+_1197nt ATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGACCAGATCTTTATGGAAAATGTA GGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATGGAACAGAAAGCTGGCCCGGCTA AAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGTTAGTGCATCTTCTCCAAGAAGG GCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTTCCAGACCTTGGTTATAACTCTG ATTGCTGTGATGGCATTTTGTGCTTTGACGATAGTTGCCCTCTATATACTTAGCTTAAAAGATCAAGACCGACGTGTCCCAAATCTCCCT CCAAGCAATATCACAAGCTCACAGGAGCCAGCTCTGCTGCCCACAGCCTCCTCCTCAGCACCTAATACATCCCTGGTAACCACACCGGCC TCCTTACAAGTACCTGAAATTACTTTCTGTGAAATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCATCCGGGGAATGAAAGAAGTCTCT TCAAGTCCTGTGCAAAGACAATCTGAGGAGAAGGAATTCCATCAGAGGCGATGGTCAGAAGACAAAAGCAAATCAGTTTTGGCAAGAAAT GCACTCAGCGGCCCTGACTGGGAGAGTGACTGGATTGATACAACCATCAGTTCTATTCAGATTATGGAAATCCAGCAAATAATAGATCAT CAGTATTGCATTCAAAGCCTCCAGTGCGGATCTGGAAATTATAATTACAATATTCCTGTTAATAAACACACACCCACCAATGTCAAGTTC TCTCTGGAAATAAACACAACAGAGCCATTGATAGTCTTCCAGTGCAAATTCACCCTTGGAAATATATGTTTCCATAGTAAAAGGGGAACC AAAGGGCTGGAAAGCCACAGAGAAATCTCCCAGGAGATGACACAGGGATATCAGCACATTTGGAGCCTCCCTGTAGCCCCATTTTCTGAC AGCATGTTCCATTTCCGTGTAGCTGCACCGGATTTAGCTGACTGTTCAACTGATCCTTATTTTGCTGGGATATTCTTCACCGATTACTTC >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000547771_chr12_70320351_+_1161nt ATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGACCAGATCTTTATGGAAAATGTA GGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATGGAACAGAAAGCTGGCCCGGCTA AAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGTTAGTGCATCTTCTCCAAGAAGG GCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTTCCAGACCTTGGTTATAACTCTG ATTGCTGTGATGGCATTTTGCTTAAAAGATCAAGACCGACGTGTCCCAAATCTCCCTCCAAGCAATATCACAAGCTCACAGGAGCCAGCT CTGCTGCCCACAGCCTCCTCCTCAGCACCTAATACATCCCTGGTAACCACACCGGCCTCCTTACAAGTACCTGAAATTACTTTCTGTGAA ATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCATCCGGGGAATGAAAGAAGTCTCTTCAAGTCCTGTGCAAAGACAATCTGAGGAGAAG GAATTCCATCAGAGGCGATGGTCAGACAAAAGCAAATCAGTTTTGGCAAGAAATGCACTCAGCGGCCCTGACTGGGAGAGTGACTGGATT GATACAACCATCAGTTCTATTCAGATTATGGAAATCCAGCAAATAATAGATCATCAGTATTGCATTCAAAGCCTCCAGTGCGGATCTGGA AATTATAATTACAATATTCCTGTTAATAAACACACACCCACCAATGTCAAGTTCTCTCTGGAAATAAACACAACAGAGCCATTGATAGTC TTCCAGTGCAAATTCACCCTTGGAAATATATGTTTCCATAGTAAAAGGGGAACCAAAGGGCTGGAAAGCCACAGAGAAATCTCCCAGGAG ATGACACAGGGATATCAGCACATTTGGAGCCTCCCTGTAGCCCCATTTTCTGACAGCATGTTCCATTTCCGTGTAGCTGCACCGGATTTA |
| * Fusion transcript sequences (Full-length transcript). |
| >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000552032_chr12_70320351_+_1591nt GAGCGGAGGCGCTGCTGCGGCGCTGCGGCCGACGCCGGGTCCGCACCAACTGTCTCCCCCTCCCAGCTTCTTACCTCGGCTTCCTACTCC TTCCCCCGCCCGCCCAGCACCGCCAGCCCGGGAGAGCTGCCGGGAGTTCCCCGGGAGCCTCAGGTGGTGACTATCCTGTTGAGAAGCAAA AGATACTTTGCAAGTAAAAAATATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGA CCAGATCTTTATGGAAAATGTAGGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATG GAACAGAAAGCTGGCCCGGCTAAAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGT TAGTGCATCTTCTCCAAGAAGGGCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTT CCAGACCTTGGTTATAACTCTGATTGCTGTGATGGCATTTTGTGCTTTGACGATAGTTGCCCTCTATATACTTAGCTTAAAAGATCAAGA CCGACGTGTCCCAAATCTCCCTCCAAGCAATATCACAAGCTCACAGGAGCCAGCTCTGCTGCCCACAGCCTCCTCCTCAGCACCTAATAC ATCCCTGGTAACCACACCGGCCTCCTTACAAGTACCTGAAATTACTTTCTGTGAAATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCAT CCGGGGAATGAAAGAAGTCTCTTCAAGTCCTGTGCAAAGACAATCTGAGGAGAAGGAATTCCATCAGAGGCGATGGTCAGAAGACAAAAG CAAATCAGTTTTGGCAAGAAATGCACTCAGCGGCCCTGACTGGGAGAGTGACTGGATTGATACAACCATCAGTTCTATTCAGATTATGGA AATCCAGCAAATAATAGATCATCAGTATTGCATTCAAAGCCTCCAGTGCGGATCTGGAAATTATAATTACAATATTCCTGTTAATAAACA CACACCCACCAATGTCAAGTTCTCTCTGGAAATAAACACAACAGAGCCATTGATAGTCTTCCAGTGCAAATTCACCCTTGGAAATATATG TTTCCATAGTAAAAGGGGAACCAAAGGGCTGGAAAGCCACAGAGAAATCTCCCAGGAGATGACACAGGGATATCAGCACATTTGGAGCCT CCCTGTAGCCCCATTTTCTGACAGCATGTTCCATTTCCGTGTAGCTGCACCGGATTTAGCTGACTGTTCAACTGATCCTTATTTTGCTGG GATATTCTTCACCGATTACTTCTTTTACTTCTATCGACGCTGTGCCTAATTTGTTCAAGTTTGGGGACTTTACCAAAGAAAAATACTCAG GAATACATTTAACAGAAACGAACATCCTCTTGCAACTTCTTTTTTCTTCTTTGTAAAACATTTACGTTTATTGCTGAAGGACTTTTTCAG >In-frame_VAMP4_ENST00000415773_chr1_171707489_-_MYRFL_ENST00000547771_chr12_70320351_+_1929nt GAGCGGAGGCGCTGCTGCGGCGCTGCGGCCGACGCCGGGTCCGCACCAACTGTCTCCCCCTCCCAGCTTCTTACCTCGGCTTCCTACTCC TTCCCCCGCCCGCCCAGCACCGCCAGCCCGGGAGAGCTGCCGGGAGTTCCCCGGGAGCCTCAGGTGGTGACTATCCTGTTGAGAAGCAAA AGATACTTTGCAAGTAAAAAATATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGA CCAGATCTTTATGGAAAATGTAGGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATG GAACAGAAAGCTGGCCCGGCTAAAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGT TAGTGCATCTTCTCCAAGAAGGGCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTT CCAGACCTTGGTTATAACTCTGATTGCTGTGATGGCATTTTGCTTAAAAGATCAAGACCGACGTGTCCCAAATCTCCCTCCAAGCAATAT CACAAGCTCACAGGAGCCAGCTCTGCTGCCCACAGCCTCCTCCTCAGCACCTAATACATCCCTGGTAACCACACCGGCCTCCTTACAAGT ACCTGAAATTACTTTCTGTGAAATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCATCCGGGGAATGAAAGAAGTCTCTTCAAGTCCTGT GCAAAGACAATCTGAGGAGAAGGAATTCCATCAGAGGCGATGGTCAGACAAAAGCAAATCAGTTTTGGCAAGAAATGCACTCAGCGGCCC TGACTGGGAGAGTGACTGGATTGATACAACCATCAGTTCTATTCAGATTATGGAAATCCAGCAAATAATAGATCATCAGTATTGCATTCA AAGCCTCCAGTGCGGATCTGGAAATTATAATTACAATATTCCTGTTAATAAACACACACCCACCAATGTCAAGTTCTCTCTGGAAATAAA CACAACAGAGCCATTGATAGTCTTCCAGTGCAAATTCACCCTTGGAAATATATGTTTCCATAGTAAAAGGGGAACCAAAGGGCTGGAAAG CCACAGAGAAATCTCCCAGGAGATGACACAGGGATATCAGCACATTTGGAGCCTCCCTGTAGCCCCATTTTCTGACAGCATGTTCCATTT CCGTGTAGCTGCACCGGATTTAGCTGACTGTTCAACTGATCCTTATTTTGCTGGGATATTCTTCACCGATTACTTCTTTTACTTCTATCG ACGCTGTGCCTAATTTGTTCAAGTTTGGGGACTTTACCAAAGAAAAATACTCAGGAATACATTTAACAGAAACGAACATCCTCTTGCAAC TTCTTTTTTCTTCTTTGTAAAACATTTACGTTTATTGCTGAAGGACTTTTTCAGGCTTTAGCTTCCAACAGTTTTGAGACATTAATGAGG AGAATAAAATGTTTGCTGAAACTTGAAATAATGTGATGTTTGATTTTGCCATGACTATGAAGAAAACATTTCCTGGAGCAAACAGTTCTG TTGAATTTAAAAATACTATTATTTCTGGTATTAAGGAAGTTGTGAGCTCAAAATAAGGAGATCTAGCCTCTATTTTGTTTTAATGTATTT TAAAGCTTTTGAAAAAACCAAAAGGGCCATGTCGACTTCGGCCCACTAAACATAGACTCTTGAGAATGTGTGATATGGTATGTGGAGGAG ATGTGGGGGGTGGTATCTGATACTGAGCTCACATTTAGGCAAATTGTCCTATGTGTGTGTGTATTGTATAAACACATACACTAGAGTACA |
Top |
FusionGenePPI for VAMP4_MYRFL |
| 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 |
| VAMP4 | AP1M1, STX4, CSNK2A1, PACS1, STX6, STX16, VTI1A, VTI1B, VPS53, VPS52, SNAP29, BCL2L13, CCDC155, STX7, STX8, STX12, CLEC12A, STX3, NAPG, STX18, TMEM17, PLK1, ZNF526, NTMT1, NAPB, NBAS, MBLAC2, COX6B1, SCFD2, USE1, STX10, HECTD4, STX11, NAPA, BNIP1, STX5, OXSM, GOSR2, GOSR1, SCFD1, VPS45, CLINT1, ZW10, GALM, SNAP23, C1orf123, LMNA | MYRFL |
| - 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 |
Top |
RelatedDrugs for VAMP4_MYRFL |
| 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 |
Top |
RelatedDiseases for VAMP4_MYRFL |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|