VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004523

Fusion event

HPV-KLF12 integration

Validated

Yes

Detection method

Multiplex RT-PCR, APOT assay

Data source

Curated

Sample type

Tumor

Disease

Cervical carcinoma (CC)

Quality evaluation

Normal

Reported year

2014

PubMed ID

23824673

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

K02718

Gene

E2

Start

2637

Integrated sequence

TGGATGTAAAGCATAGAC CATTGGTACAACTAAAATGCCCTCCATTATTAATTACATCTAACATTAATGCTGGTACAGATTCTAGGTG GCCTTATTTA| |CATAATAGATTGGTGGTGTTTACATTTCCTAATGAGTTTCCATTTGACGAAAACGGAAAT CCAGTGTATGAGCTTAATGATAAGAACTGGAAATCCTTT

Host Sequence

Chromosome

chr13

Cytoband

q22.2

Reference genome

GRCh37/hg19

Start

74255979/73681842 (Hg38)

End

74255979/73681842 (Hg38)

Location type

Intronic

Fragile sites / regions

FRA13E

Target gene

KLF12

miRNAs that regulate target gene

hsa-mir-101-3p ; hsa-mir-23a-3p ; hsa-mir-4652-3p ; hsa-mir-4743-3p ; hsa-mir-218-5p ; hsa-mir-4679 ; hsa-mir-4677-3p ; hsa-mir-216b-5p ; hsa-mir-1264 ; hsa-mir-6888-3p ; hsa-mir-4775 ; hsa-mir-215-3p ; hsa-mir-6773-3p ; hsa-mir-34a-5p ; hsa-mir-141-3p ; hsa-mir-137 ; hsa-mir-200a-3p ; hsa-mir-4720-3p ; hsa-mir-4804-3p

Nearest miRNA

hsa-mir-1297/Upstream/7463518; hsa-mir-1267/Downstream/4016170;

Nearest TSS

ENST00000623511/Upstream/33589; ENST00000419499/Downstream/313207;

Nearest CpG islands

None/Target, chr13-CpG: 551/Upstream/621610, chr13-CpG: 31/Downstream/452130

Upstream sequence

acccccatgatccaatcacctcccactaaggcccaactccaacatacaggattgcaactgaacatgagatttgggtgaggacacagatccaaaccatatc

Downstream sequence

aGCATCAAAAGAAGGTGGAAGTAAGAATAAATAAAGTCCACATATGGGTAAAGTTTTAATTTTAGCATGATGATGAAAGAATAAAGAAGAAATGTACATa

Reference

Lu, X., et al. Multiple-integrations of HPV16 genome and altered transcription of viral oncogenes and cellular genes are associated with the development of cervical cancer. PLoS One ,2014,9(7): e97588.