VISDB - VIS Detail

Basic Information

VIS ID

TVIS30003677

Fusion event

HIV-NFKB1 integration

Validated

No

Detection method

QiaQuick PCR and Sequencing

Data source

download(RID)

Sample type

Cell line

Disease

HIV-infected disease (HID)

Quality evaluation

Normal

Reported year

2013

PubMed ID

23953889

Virus Sequence

Virus name

HIV

Reference genome

Not given

Host Sequence

Chromosome

chr4

Cytoband

q24

Reference genome

GRCh37/hg19

Start

103525429/102604272 (Hg38)

End

103525429/102604272 (Hg38)

Orient

-

Location type

Intronic

Target gene

NFKB1

miRNAs that regulate target gene

hsa-mir-9-5p ; hsa-mir-146a-5p ; hsa-mir-146b-5p ; hsa-mir-15a-5p ; hsa-let-7a-5p ; hsa-mir-16-5p ; hsa-mir-21-5p ; hsa-mir-155-5p ; hsa-mir-26b-5p ; hsa-mir-92a-3p ; hsa-mir-508-3p ; hsa-mir-199a-5p ; hsa-mir-139-5p ; hsa-mir-138-5p ; hsa-mir-9-3p ; hsa-mir-339-3p ; hsa-mir-34a-5p

Nearest miRNA

hsa-mir-12113/Upstream/1273858; hsa-mir-1243/Downstream/6884426;

Nearest TSS

ENST00000502981/Upstream/11023; ENST00000501133/Downstream/46566;

Nearest CpG islands

None/Target, chr4-CpG: 46/Upstream/102200, chr4-CpG: 54/Downstream/156407

Nearest cancer related gene

NFKB1(TSG, No orient, 0)

Upstream sequence

AAGTACTGGATACAAATGTACGTATACTTGAAATACATAGATATTTTCATATACTCTCACATACAATCCACATTATATTAAATGTACTTCTCTTGCCTTG

Downstream sequence

CATTAACCtttaaaatttttttaatttaatttaattataGATTCAAAGGAGGTTACAAAAACGTACTAGGAAGTCCTAGTATTTACTGCAAGGAAACCAG

Reference

Sherrill-Mix, S., et al. HIV latency and integration site placement in five cell-based models.2013, Retrovirology 10: 90.