VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS20004615

Fusion event

HPV-TRMO integration

Validated

Yes

Detection method

FISH, WGS, RNA-seq, qPCR

Data source

Curated

Sample type

Tumor

Disease

Cervical carcinoma (CC)

Quality evaluation

Perfect

Reported year

2014

PubMed ID

24201445

Virus Sequence

Virus name

HPV

Subtype

HPV16

Reference genome

NC_001526.2

Gene

E1

Start

1968

End

2062

Integrated sequence

TAGTAGACGATAGTGAAATTGCATATAAATATGCACAATTGGCAGACACTAATAGTAATGCAAGTGCCTTTCTAAAAAGTAATTCACAGGCAAAA

Host Sequence

Chromosome

chr9

Cytoband

q22.33

Reference genome

GRCh37/hg19

Start

100676884/97914578 (Hg38)

End

100676860/97914602 (Hg38)

Location type

Intronic

Target gene

TRMO

miRNAs that regulate target gene

hsa-mir-5096 ; hsa-mir-3187-3p ; hsa-mir-4435 ; hsa-mir-588 ; hsa-mir-4701-5p ; hsa-mir-548s ; hsa-mir-197-3p ; hsa-mir-4755-3p ; hsa-mir-98-5p ; hsa-mir-4500 ; hsa-mir-4458 ; hsa-let-7i-5p ; hsa-let-7g-5p ; hsa-let-7f-5p ; hsa-let-7e-5p ; hsa-let-7d-5p ; hsa-let-7c-5p ; hsa-let-7b-5p ; hsa-let-7a-5p ; hsa-mir-4716-5p ; hsa-mir-4781-3p ; hsa-mir-296-3p ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-562 ; hsa-mir-6818-5p ; hsa-mir-190a-3p ; hsa-mir-6820-3p ; hsa-mir-3164 ; hsa-mir-3118 ; hsa-mir-134-5p ; hsa-mir-16-1-3p ; hsa-mir-511-3p ; hsa-mir-5011-5p ; hsa-mir-5580-3p ; hsa-mir-1277-5p ; hsa-mir-6867-5p ; hsa-mir-7703 ; hsa-mir-6720-5p ; hsa-mir-6512-3p ; hsa-mir-6729-5p ; hsa-mir-4649-5p ; hsa-mir-661 ; hsa-mir-4696 ; hsa-mir-4486 ; hsa-mir-766-3p ; hsa-mir-939-3p ; hsa-mir-6849-3p ; hsa-mir-451b ; hsa-mir-508-5p ; hsa-mir-4432 ; hsa-mir-1276 ; hsa-mir-1273h-5p ; hsa-mir-149-3p ; hsa-mir-1827 ; hsa-mir-1910-3p ; hsa-mir-30b-3p ; hsa-mir-3192-5p ; hsa-mir-3612 ; hsa-mir-3689a-3p ; hsa-mir-3689b-3p ; hsa-mir-3689c ; hsa-mir-4537 ; hsa-mir-455-3p ; hsa-mir-4728-5p ; hsa-mir-4756-3p ; hsa-mir-490-3p ; hsa-mir-5186 ; hsa-mir-650 ; hsa-mir-6511a-5p ; hsa-mir-6516-5p ; hsa-mir-6779-5p ; hsa-mir-6780a-5p ; hsa-mir-6785-5p ; hsa-mir-6799-5p ; hsa-mir-6883-5p ; hsa-mir-7106-5p ; hsa-mir-7851-3p

Nearest miRNA

hsa-let-7a-1/Upstream/550897; hsa-mir-12126/Downstream/314547;

Nearest TSS

ENST00000422679/Upstream/2107; ENST00000473205/Downstream/7866;

Nearest CpG islands

None/Target, chr9-CpG: 64/Upstream/56668, chr9-CpG: 53/Downstream/7614

Downstream sequence

TTATAATAACTGTGACAAACCCCCT

Target sequence

gggggtttgtcacagttattataa

Junction sequence

ATAGTAGACGATAGTGAAATTGCATATAAATATGCACAATTGGCAGACACTAATAGTAATGCAAGTGCCTTTCTAAAAAGTAATTCACAGGCAAAGAGTCCAGGGCTGCGTGATTATAATAACTGTGACAAACCCCCT

* Color: Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence

Reference

Akagi, K., et al.Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res ,2014,24(2): 185-199.