VISDB - VIS Detail

Basic Information

VIS ID

TVIS30016461

Fusion event

HIV-CDK19 integration

Validated

Yes

Detection method

LM PCR

Data source

Curated

Sample type

PBMC

Disease

HIV-infected disease (HID)

Quality evaluation

Good

Reported year

2014

PubMed ID

24968937

Virus Sequence

Virus name

HIV

Reference genome

Not given

Host Sequence

Chromosome

chr6

Cytoband

q21

Reference genome

GRCh37/hg19

Start

110972532/110651329 (Hg38)

End

110972809/110651329 (Hg38)

Orient

Location type

Intronic

Fragile sites / regions

FRA6F

Target gene

CDK19

miRNAs that regulate target gene

hsa-mir-373-3p ; hsa-mir-18a-5p ; hsa-mir-335-5p ; hsa-mir-130b-3p ; hsa-mir-128-3p ; hsa-mir-148a-3p ; hsa-mir-26b-5p ; hsa-mir-21-5p ; hsa-mir-19b-3p ; hsa-mir-10a-5p ; hsa-mir-20a-5p ; hsa-mir-106a-3p ; hsa-mir-526b-5p ; hsa-mir-4276 ; hsa-mir-382-3p ; hsa-mir-148b-3p ; hsa-mir-152-3p ; hsa-mir-3666 ; hsa-mir-454-3p ; hsa-mir-130a-3p ; hsa-mir-4295 ; hsa-mir-301a-3p ; hsa-mir-301b-3p ; hsa-mir-4309 ; hsa-mir-3198 ; hsa-mir-6880-5p ; hsa-mir-7847-3p ; hsa-mir-122-5p ; hsa-mir-504-3p ; hsa-mir-6851-5p ; hsa-mir-3689d ; hsa-mir-3202 ; hsa-mir-4533 ; hsa-mir-6086 ; hsa-mir-377-5p ; hsa-mir-6500-3p ; hsa-mir-3614-5p ; hsa-mir-619-3p ; hsa-mir-490-3p ; hsa-mir-4671-3p ; hsa-mir-548x-5p ; hsa-mir-548g-5p ; hsa-mir-548f-5p ; hsa-mir-548aj-5p ; hsa-mir-548p ; hsa-mir-665 ; hsa-mir-7160-5p ; hsa-mir-4722-5p ; hsa-mir-6884-5p ; hsa-mir-485-5p ; hsa-mir-1827 ; hsa-mir-4649-3p ; hsa-mir-4768-3p ; hsa-mir-4478 ; hsa-mir-4419b ; hsa-mir-3929 ; hsa-mir-940 ; hsa-mir-6893-5p ; hsa-mir-6808-5p ; hsa-mir-34b-3p

Nearest miRNA

hsa-mir-10398/Upstream/3867109; hsa-mir-1202/Downstream/8417718;

Nearest TSS

ENST00000381078/Upstream/173422; ENST00000368877/Downstream/94872;

Nearest CpG islands

None/Target, chr6-CpG: 120/Upstream/4709, chr6-CpG: 135/Downstream/162983

Upstream sequence

ctactatctatctatctatctatctatctatctatccgtctaacacctatttatgtatctgtctgtctaactatctTCCTCCTGCCCAATTTCTGATGGC

Downstream sequence

gtattttaatatttttacaactacactcataggtgaggttgacctgaaatttttatttttcatgctttgtctggttttgctatcaagattatactggctt

Target sequence

AGAGGATTTGAAGAGACTATCACTTCTAGTACACTAAATATTTCTCTAATGTTTGCTTTTGTCTATTTTGGTATTGCTTATAATTAGAGAAATGGCATTTTAAAACACATAATAAAAAATAggccgggcacgatggcacaactctgtaatcccagtactttgggaggccgagaagggcagattgcttgcgctcaggagtttgaaaccaggctgggcaacatggtgaaaaccccatctctaaaaaaaatacaTTCG

Reference

Maldarelli, F., et al. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science,2014, 345(6193): 179-183.