VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004163

Fusion event

HPV-PAWR integration

Validated

Yes

Detection method

APOT and sequencing

Data source

Curated

Sample type

Cell line

Disease

Cervical carcinoma (CC)

Quality evaluation

Good

Reported year

2018

PubMed ID

29364907

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

AF125673.1

Strand

-

Gene

L2

Start

4212

End

4418

Orient

-

Integrated sequence

AATAAACTGTTATCACTTAACAATGCGACACAAACGTTCTGCAAAACGCACAAAACGTGCATCGGCTACCCAACTTTATAAAACATGCAAACAGGCAGGTACATGTCCACCTGACATTATACCTAAGGTTGAAGGCAAAACTATTGCTGATCAAATATTACAATATGGAAGTATGGGTGTATTTTTTGGTGGGTTAGGAATTGGAAC

Host Sequence

Chromosome

chr12

Cytoband

q21.2

Reference genome

GRCh37/hg19

Start

80007755/79613975 (Hg38)

End

80007807/79614027 (Hg38)

Orient

+

Location type

Intronic

Target gene

PAWR

miRNAs that regulate target gene

hsa-mir-215-5p ; hsa-mir-192-5p ; hsa-mir-8084 ; hsa-mir-621 ; hsa-mir-3692-3p ; hsa-mir-1179 ; hsa-mir-5047 ; hsa-mir-218-5p ; hsa-mir-7156-3p ; hsa-mir-1301-3p ; hsa-mir-367-3p ; hsa-mir-25-3p ; hsa-mir-92a-3p ; hsa-mir-363-3p ; hsa-mir-32-5p ; hsa-mir-92b-3p ; hsa-mir-103a-3p ; hsa-mir-107 ; hsa-mir-101-5p ; hsa-mir-591 ; hsa-mir-6512-5p ; hsa-mir-6869-5p ; hsa-mir-496 ; hsa-mir-4461 ; hsa-mir-590-3p ; hsa-mir-1252-3p ; hsa-mir-3646 ; hsa-mir-3611 ; hsa-mir-4282 ; hsa-mir-203b-3p ; hsa-mir-7158-3p ; hsa-mir-493-3p ; hsa-mir-4680-5p ; hsa-mir-186-3p ; hsa-mir-4733-5p ; hsa-mir-3607-5p ; hsa-mir-570-5p ; hsa-mir-548ba ; hsa-mir-548ai ; hsa-mir-548ag ; hsa-mir-548l ; hsa-mir-548n ; hsa-mir-653-5p ; hsa-mir-1267 ; hsa-mir-124-5p ; hsa-mir-488-5p ; hsa-mir-95-5p ; hsa-mir-4307 ; hsa-mir-5586-5p ; hsa-mir-8066 ; hsa-mir-30e-5p ; hsa-mir-30c-5p ; hsa-mir-30d-5p ; hsa-mir-30b-5p ; hsa-mir-30a-5p

Nearest miRNA

hsa-let-7i/Upstream/194654; hsa-mir-1178/Downstream/1218506;

Nearest TSS

ENST00000382841/Upstream/15993; ENST00000551995/Downstream/18135;

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/809355, chr12-CpG: 198/Downstream/75724

Nearby gene

MIR5692B(-155315) ;

Nearest cancer related gene

PAWR(TSG, No orient, 0)

Upstream sequence

GAAGTTCTTAGGGAGCCACAGTATTTACAGGAAACTAATTCACACTAAACTCACTTGTACTGCATTGTTTCCTGCTATGATAAAGCAAATGGGTTATGTA

Downstream sequence

gagaaggagtttcactcttgttgcccaggctacagtgcaatggtgtcatctgggctcaccgcaacctctgcctcccgggttcaagtgattctcctgcctc

Target sequence

tatatttttttttttttttttttttttttttttttttttttttttttttttt

Reference

Warburton, A., et al. HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression. PLoS Genet ,2018,14(1): e1007179.