| Basic Information ▶ | |
| VISDB ID | TVIS10051520 |
|---|---|
| Fusion Name | HBV-PTPRG-AS1 integration |
| Validated | No |
| Curated Way | Curated |
| Method | EBV capture sequencing, followed by Viral Integration Pathway Analysis (VIPA) pipeline |
| Wet Assay | No |
| Sample ID | SRR3104968.4 |
| Sample Name | SRA335342 |
| Sample Type | Tumor |
| Age | - |
| Gender | - |
| Disease Information ▶ | |
| Disease Name | Hepatocellular carcinoma |
| Disease Abbreviation | HCC |
| Cancer | Yes |
| Literature ▶ | |
| PubMed ID | 35968887 |
| Journal | Clinical and Translational Medicine |
| Published Year | 2022 |
| Human Genome ▶ | |
| Human Genome Version Description | GRCh38/hg38 |
| Human Genome RefSeq Accession | GCF_000001405.40 |
| Human Chromosome | chr3 |
| Cytogenetic Band | p14.2 |
| Human Strand | + |
| Human Integration Location Type | intronic |
| Hg19 Start | - |
| Hg19 End | - |
| Hg38 Start | 62231856 |
| Hg38 End | 62231856 |
| Junction Sequence | ctaatcaTCTCATGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGTGTTCTGGATAGTTTGAATACTTGGAAAAATTATTGTCctggaaagagttatagtaaatgttt |
| Target Gene ▶ | |
| Target Gene | PTPRG-AS1, PTPRG |
| Nearby Gene | - |
| Distance | - |
| Virus Information ▶ | |
| Virus Name | Hepatitis B virus |
| Virus Subtype Name | - |
| Virus Genome Accession | AB014381 |
| TaxonomyID | 10407 |
| Virus Abbreviation | HBV |
| Virus Genome | Hepatitis B virus 22Y04HCC genomic DNA, complete sequence |
| Virus Genome Length | 3215 bp |
| Virus Breakpoint1 | 1895 |
| Virus Breakpoint2 | - |
| Virus Gene Name | C |
| Virus Region Type | - |
| Integrated Virus Sequence | - |
| ViMIC ID | - |
| Predicted VIS Effect ▶ | |
| Region | intron |
| Impact | intronic_insertion |
| Transcript | Transcript 1: ENST00000474889.6, Transcript 2: ENST00000295874.14, Transcript 3: ENST00000475012.5, Transcript 4: ENST00000817058.1, Transcript 5: ENST00000661510.1, Transcript 6: ENST00000665590.1, Transcript 7: ENST00000817057.1 |
| Transcript 1 Gene Id | ENSG00000144724.20 |
| Transcript 1 Gene Name | PTPRG |
| Transcript 2 Gene Id | ENSG00000144724.20 |
| Transcript 2 Gene Name | PTPRG |
| Transcript 3 Gene Id | ENSG00000144724.20 |
| Transcript 3 Gene Name | PTPRG |
| Transcript 4 Gene Id | ENSG00000241472.9 |
| Transcript 4 Gene Name | PTPRG-AS1 |
| Transcript 5 Gene Id | ENSG00000241472.9 |
| Transcript 5 Gene Name | PTPRG-AS1 |
| Transcript 6 Gene Id | ENSG00000241472.9 |
| Transcript 6 Gene Name | PTPRG-AS1 |
| Transcript 7 Gene Id | ENSG00000241472.9 |
| Transcript 7 Gene Name | PTPRG-AS1 |
| SpliceAI Score | |
| Delta Scores | Acceptor Gain: 0.010 | Acceptor Loss: 0.000 | Donor Gain: 0.040 | Donor Loss: 0.000 |
| Delta Score Max | 0.040 |
| Delta Position at Max | -404 |
| Delta Score Flag | LOW |
| Gene | PTPRG |
| AlphaGenome Analysis | |
| Window | chr3:62166320-62297392 |
| RNA-seq Change (±2kb) | Mean: 3.8198351830942556e-05 | Peak: 0.0859375 |
| ATAC Change (±2kb) | Mean: 0.0009860716527327895 | Peak: 7.937493324279785 |
| Interpretation | RNA-seq: no signal in region (REF≈0, ALT≈0) | Splice sites: no signal in region (REF≈0, ALT≈0) | ATAC: minimal change 2.6% |
| 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