| Basic Information ▶ | |
| VISDB ID | TVIS20038834 |
|---|---|
| Fusion Name | HPV-TMEFF2 integration |
| Validated | No |
| Curated Way | Curated |
| Method | High-throughput Viral Integration Detection method |
| Wet Assay | Yes |
| Sample ID | - |
| Sample Name | S100 |
| Sample Type | Tumor |
| Age | 57 = 59; >57 = 50 |
| Gender | - |
| Disease Information ▶ | |
| Disease Name | Oropharyngeal squamous cell carcinoma |
| Disease Abbreviation | OPSCC |
| Cancer | Yes |
| Literature ▶ | |
| PubMed ID | 38279874 |
| Journal | Clinical and Translational Medicine |
| Published Year | 2024 |
| Human Genome ▶ | |
| Human Genome Version Description | GRCh37/hg19 |
| Human Genome RefSeq Accession | GCF_000001405.13 |
| Human Chromosome | chr2 |
| Cytogenetic Band | q32.3 |
| Human Strand | - |
| Human Integration Location Type | intronic |
| Hg19 Start | 192881887 |
| Hg19 End | 192881887 |
| Hg38 Start | 192017161 |
| Hg38 End | 192017161 |
| Junction Sequence | GCACCAACATCTGTACCTTCCATTCCCCCAGATGTATCAGGATTTAGTATTACTACTTCAACTGATACCACACCTGCTATATTAGATATTAATAATACTGTTACTACTGTTACTACACATAATAATCCCACTTTTCCTGAGGCCTGGTAACTCTCAAAGGAGACCCTGTTGCAGGCATTAGCAAT |
| Target Gene ▶ | |
| Target Gene | TMEFF2, CAVIN2-AS1 |
| Nearby Gene | - |
| Distance | - |
| Virus Information ▶ | |
| Virus Name | Human Papillomavirus |
| Virus Subtype Name | HPV16 |
| Virus Genome Accession | AF534061 |
| TaxonomyID | 10566 |
| Virus Abbreviation | HPV |
| Virus Genome | Human papillomavirus type 16 East Asian type, complete genome |
| Virus Genome Length | 7905 bp |
| Virus Breakpoint1 | 4723 |
| Virus Breakpoint2 | - |
| Virus Gene Name | HpV16gp7_L2 |
| Virus Region Type | - |
| Integrated Virus Sequence | - |
| ViMIC ID | - |
| Predicted VIS Effect ▶ | |
| Region | intron |
| Impact | intronic_insertion |
| Transcript | Transcript 1: ENST00000424116.8, Transcript 2: ENST00000792812.1, Transcript 3: ENST00000428980.6, Transcript 4: ENST00000392314.5, Transcript 5: ENST00000272771.10, Transcript 6: ENST00000877059.1, Transcript 7: ENST00000936875.1, Transcript 8: ENST00000877060.1, Transcript 9: ENST00000936874.1 |
| Transcript 1 Gene Id | ENSG00000233766.9 |
| Transcript 1 Gene Name | CAVIN2-AS1 |
| Transcript 2 Gene Id | ENSG00000233766.9 |
| Transcript 2 Gene Name | CAVIN2-AS1 |
| Transcript 3 Gene Id | ENSG00000233766.9 |
| Transcript 3 Gene Name | CAVIN2-AS1 |
| Transcript 4 Gene Id | ENSG00000144339.13 |
| Transcript 4 Gene Name | TMEFF2 |
| Transcript 5 Gene Id | ENSG00000144339.13 |
| Transcript 5 Gene Name | TMEFF2 |
| Transcript 6 Gene Id | ENSG00000144339.13 |
| Transcript 6 Gene Name | TMEFF2 |
| Transcript 7 Gene Id | ENSG00000144339.13 |
| Transcript 7 Gene Name | TMEFF2 |
| Transcript 8 Gene Id | ENSG00000144339.13 |
| Transcript 8 Gene Name | TMEFF2 |
| Transcript 9 Gene Id | ENSG00000144339.13 |
| Transcript 9 Gene Name | TMEFF2 |
| SpliceAI Score | |
| Delta Scores | Acceptor Gain: 0.050 | Acceptor Loss: 0.000 | Donor Gain: 0.000 | Donor Loss: 0.000 |
| Delta Score Max | 0.050 |
| Delta Position at Max | -377 |
| Delta Score Flag | LOW |
| Gene | TMEFF2 |
| AlphaGenome Analysis | |
| Window | chr2:191951625-192082697 |
| RNA-seq Change (±2kb) | Mean: 0.00024752598255872726 | Peak: 0.042236328125 |
| ATAC Change (±2kb) | Mean: 0.0010494254529476166 | Peak: 2.03123140335083 |
| Interpretation | RNA-seq: no signal in region (REF≈0, ALT≈0) | Splice sites: no signal in region (REF≈0, ALT≈0) | ATAC: minimal change 3.9% |
| Visualization | |
Center for Precision Health
McWilliams School of Biomedical Informatics at UTHealth Houston
7000 Fannin Street, Suite 600, Houston, TX 77030
Email: Zhongming Zhao, Ph.D