hsa-mir-3199 _LIHC.png
TNFSF10 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000440
Fusion event
AAV2-TNFSF10 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2015
PubMed ID
26301494
Virus Sequence
Virus name
AAV2
Reference genome
AF043303.1
Start
4270
End
4571
Orient
+
Integrated sequence
ACAGCAAACGCTGGAATCCCGAAATTCAGTACACTTCCAACTACAACAAGTCTGTTAATGTGGACTTTACTGTGGACACTAATGGCGTGTATTCAGAGCCTCGCCCCATTGGCACCAGATACCTGACTCGTAATCTGTAATTGCTTGTTAATCAATAAACCGTTTAATTCGTTTCAGTTGAACTTTGGTCTCTGCGTATTTCTTTCTTATCTAGTTTCCATGGCTACGTAGATAAGTAGCATGGCGGGTTAATCA
Host Sequence
Chromosome
chr3
Cytoband
q26.31
Reference genome
GRCh37/hg19
Start
172224027/172506236 (Hg38)
End
172224026/172506237 (Hg38)
Orient
+
Location type
Intronic
Target gene
TNFSF10
miRNAs that regulate target gene
hsa-mir-222-3p ; hsa-mir-221-3p ; hsa-mir-98-5p ; hsa-mir-25-3p ; hsa-mir-1297 ; hsa-mir-26a-5p ; hsa-mir-26b-5p ; hsa-mir-3152-5p ; hsa-mir-3199 ; hsa-mir-365a-5p ; hsa-mir-365b-5p ; hsa-mir-4465 ; hsa-mir-513c-5p ; hsa-mir-514b-5p ; hsa-mir-562 ; hsa-mir-5697 ; hsa-mir-6819-3p ; hsa-mir-6836-3p ; hsa-mir-6877-3p ; hsa-mir-8052
Nearest miRNA
hsa-let-7g/Upstream/1399477; hsa-mir-1224/Downstream/2863303;
Nearest TSS
ENST00000440867/Upstream/57780; ENST00000366254/Downstream/17073;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/56160, chr3-CpG: 39/Downstream/204389
Upstream sequence
GACCAAAACAAACAAACAGAAAACAGAAAACAAAAAAACCTCTATGCAATCTGAGTAGAGCAGCCACAACCAAAAAATTCTACAACACACACTGTTCTGAAAGTGACTCACTTATCCCAAGAGAATGAAATTGCTGAAAGATCTTTCAGGACTCTACCTCATATCAGTT
Downstream sequence
CCCTCTCTAGCAGAAATCTAGAAGACTGTCAGCTTCCAAACATTAATGCAATGGTTAACATCTTCTGTCTTTATAATCTACTCCTTGTAAAGACTGTAGAAGAAAGAGCAACAATCCATCTCTCAAGTAGTGTATCACAGTAGTAGCCTCCAGGTTTCCTTAAGGGACAACATCCTTAAGTCAAAAGAGAGA
Junction sequence
GACCAAAACAAACAAACAGAAAACAGAAAACAAAAAAACCTCTATGCAATCTGAGTAGAGCAGCCACAACCAAAAAATTCTACAACACACACTGTTCTGAAAGTGACTCACTTATCCCAAGAGAATGAAATTGCTGAAAGATCTTTCAGGACTCTACCTCATATCAGTTTGTGAACAGCAAACGCTGGAATCCCGAGATTCAGTACACTTCCAACTACAACAAATCTGTTAATGTGGACTTTACTGTGGACACTAATGGTGTGTATTCAGAGCCTCGCCCCATTGGCACCAGATACCTGACTCGTAATCTGTAATTGCTTGTTAATCAATAAACCGTGTAATTCGTTTCAGTTGAACTTTGGTCTCCGCGTACTTCTTTTCTTATCTAGTTTCCATGGCTACGTAGATAAGTAGCATGGCGGGTTAATCATTAACCACAAGGAACCCCTAGTGATGGAGTTGGCCACTCCCTCTCTAGCAGAAATCTAGAAGACTGTCAGCTTCCAAACATTAATGCAATGGTTAACATCTTCTGTCTTTATAATCTACTCCTTGTAAAGACTGTAGAAGAAAGAGCAACAATCCATCTCTCAAGTAGTGTATCACAGTAGTAGCCTCCAGGTTTCCTTAAGGGACAACATCCTTAAGTCAAAAGAGAGA
* 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.
Curate