Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000438
Fusion event
AAV2-CCNA2 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2015
PubMed ID
Virus Sequence
Virus name
AAV2
Reference genome
Start
2611
End
4585
Orient
+
Integrated sequence
AGACGGCTCCGGGAAAAAAGAGGCCGGTAGAGCACTCTCCTGTGGAGCCAGACTCCTCCTCGGGAACCGGAAAGGCGGGCCAGCAGCCTGCAAGAAAAAGATTGAATTTTGGTCAGACTGGAGACGCAGACTCAGTACCTGACCCCCAGCCTCTCGGACAGCCACCAGCAGCCCCCTCTGGTCTGGGAACTAATACGATGGCTACAGGCAGTGGCGCACCAATGGCAGACAATAACGAGGGCGCCGACGGAGTGG
Host Sequence
Chromosome
chr4
Cytoband
q27
Reference genome
End
122742409/121821262 (Hg38)
Orient
-
Location type
Intronic
Target gene
miRNAs that regulate target gene
hsa-mir-24-3p ; hsa-let-7b-5p ; hsa-mir-146a-5p ; hsa-mir-193b-3p ; hsa-mir-132-3p ; hsa-mir-212-3p ; hsa-mir-98-5p ; hsa-mir-197-3p ; hsa-mir-10b-3p ; hsa-mir-130b-3p ; hsa-mir-27b-3p ; hsa-mir-548aw ; hsa-mir-1468-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-1825 ; hsa-mir-4676-5p ; hsa-mir-575 ; hsa-mir-548e-5p ; hsa-mir-148a-3p ; hsa-mir-152-3p ; hsa-mir-148b-3p ; hsa-mir-4295 ; hsa-mir-130a-3p ; hsa-mir-301b-3p ; hsa-mir-3666 ; hsa-mir-454-3p ; hsa-mir-301a-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-6835-3p ; hsa-mir-29c-3p ; hsa-mir-29a-3p ; hsa-mir-29b-3p ; hsa-mir-22-3p
Nearest miRNA
hsa-mir-12113/Upstream/7164400; hsa-mir-1305/Downstream/3685997;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/19651, chr4-CpG: 71/Downstream/2140
Upstream sequence
AACAGAACCACCATGCCATTTGCTCCTTTCTGTTGTGGAAGATGGATACTTTAAGATAATACCTGATTCTCATTTTCCTGTTAGGGGCCTACCAATATGTTTTTTTTTTTTTCCCTCATTAACTAAAATCATTCCAAAGTTCTATGTAC
Downstream sequence
GGCCACTCCCTCTCTGCGCGCTCGCTCGCAGACTAGGGTAAAATATTCTACATATTTTGTCATGAGAAGCTCTTTTTAGTTTGAAGAAATAAGTGCTTTGTTAATATGAGATTCCTTCCATGGCAGTCATTTTTAGCTATTAAACTAAATAGGCAAACAATTAATTTAAT
Target sequence
GATACTG
Junction sequence
AACAGAACCACCATGCCATTTGCTCCTTTCTGTTGTGGAAGATGGATACTTTAAGATAATACCTGATTCTCATTTTCCTGTTAGGGGCCTACCAATATGTTTTTTTTTTTTTCCCTCATTAACTAAAATCATTCCAAAGTTCTATGTACAGAAAACGGCTCCGGGAAAAAAGAGGCCGGTAGAGCACTCTCCTGTGGAGCCAGACTCCTCCTCGGGAACCGGGAAAGCGGGCCAGCAGCCTGCAAGAAAGAGATTGAATTTTGGTCAGACTGGAGACGCAGACTCCGTACCTGACCCCCAGCCTCTCGGACAGCCACCAGCAGCCCCCTCTGGTCTGGGAACTAATACGATGGCTACAGGCAGTGGCGCACCAATGGCAGACAATAACGAGGGCGCCGACGGAGTGGGTAATTCCTCGGGAAATTGGCATTGCGATTCCACATGGATGGGCGACAGAGTCATCACCACCAGCACCCGCACCTGGGCTCTGCCCACCTACAACAACCATCTGTACAAACAGATTTCCAGCCAATCAGGAGCCAGCAACGACAACCACTACTTTGGCTACAGCACCCCCTGGGGGTATTTTGACTTCAACAGATTCCACTGCCACTTTTCACCACGTGACTGGCAAAGACTCATCAACAACAACTGGGGATTCCGACCAAAAAGACTCAACTTCAAGCTCTTTAACATTCAAGTCAAGGAGGTCACGCAGAATGACGGTACGACAACGATTGCCAATAACCTTACCAGCACGGTTCAGGTGTTTACTGACTCGGAGTACCAGCTCCCGTACGTCCTCGGCTCGGCGCATCAAGGATGCCTCCCGCCGTTCCCAGCAGACGTCTTCATGGTGCCACAGTATGGATACCTCACCCTGAACAACGGGAGTCAGGCAGTAGGACGCTCTTCATTTTACTGCCTGGAGTACTTTCCTTCTCAGATGCTTCGTACCGGAAACAACTTTACCTTCAGCTACACCTTTGAAGACGTGCCTTTCCACAGCAGCTACGCTCACAGTCAAAGTCTGGACCGTCTCATGAATCCTCTCATCGACCAGTACCTGTATTACTTGAGCAGAACAAACACTCCAAGCGGAACCACCACGCAGTCCAGGCTTCAGTTTTCTCAGGCCGGAGCGAGTGACATTCGGGACCAGTCTAGGAACTGGCTTCCTGGACCCTGTTACCGCCAGCAGCGAGTATCAAAGACAGCTGCGGACAACAACAACAGTGAATACTCGTGGACTGGAGCTACCAAGTACCACCTCAATGGCAGAGACTCTCTGGTGAATCCGGGCCCGGCCATGGCCAGCCACAAGGACGATGAAGAAAAGTTTTTTCCTCAAAGCGGGGTTCTCATCTTTGGGAAGCAAGGCTCAGAGAAAACAAATGTGGACATTGAAAAGGTCATGATTACAGACGAAGAGGAAATCAGGACCACCAATCCCGTGGCTACGGAGCAGTATGGTTCTGTATCTACCAACCTCCAGAGCGGCAACACACAAGCAGCTACCGCAGATGTCAACACACAAGGCGTTCTTCCAGGCATGGTCTGGCAGGACAGAGACGTGTACCTGCAGGGGCCTATCTGGGCAAAGATTCCACACACGGACGGACATTTTCACCCCTCTCCCCTCATGGGCGGATTTGGACTTAAACACCCTCCTCCACAGATTCTCATCAAGAACACCCCGGTACCTGCAAATCCTTCGACCACCTTCAGTGCGGCAAAGTTTGCTTCTTTCATCACACAGTATTCCACGGGACAGGTCAGCGTGGAGATCGAGTGGGAGCTGCAGAAGGAGAACAGCAAACGTTGGAATCCCGAGATTCAGTACACTTCCAACTACAATAAATCTGTTAATGTGGACTTTACTGTGGACACTAATGGTGTGTATTCAGAGCCTCGCCCCATTGGCACCAGATACCTGACTCGTAATCTGTAATTGCTTGTTAATCAATAAACCGTTTAATTCGTTTCAGTTGAACTTTGGTCTCTGCGTATCTCTTTCTTATCTAGTTTCCATGGCTACGTAGATAAGTACCATGGCGGGTTAATCATTAACTCTAAGGAACCCCTAGTGATGGAGTTGGCCACTCCCTCTCTGCGCGCTCGCTCGCAGACTAGGGTAAAATATTCTACATATTTTGTCATGAGAAGCTCTTTTTAGTTTGAAGAAATAAGTGCTTTGTTAATATGAGATTCCTTCCATGGCAGTCATTTTTAGCTATTAAACTAAATAGGCAAACAATTAATTTAAT
* Color:
Human Sequence
/
Virus Sequence
/
Overlapped sequence
/
Unknown sequence
Reference
Nault, J. C., et al. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas. Nat Genet ,2015,47(10): 1187-1193.