VISDB - VIS Detail

Basic Information

VIS ID

TVIS30014987

Fusion event

HIV-ATXN2 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

chr12

Cytoband

q24.12

Reference genome

GRCh37/hg19

Start

111956942/111519138 (Hg38)

End

111957419/111519138 (Hg38)

Orient

Location type

Intronic

Fragile sites / regions

FRA12E

Target gene

ATXN2

miRNAs that regulate target gene

hsa-mir-1226-3p ; hsa-let-7b-5p ; hsa-mir-374b-3p ; hsa-mir-4524b-5p ; hsa-mir-4524a-5p ; hsa-mir-4519 ; hsa-mir-4274 ; hsa-mir-6796-5p ; hsa-mir-4507 ; hsa-mir-3940-5p ; hsa-mir-6819-5p ; hsa-mir-6812-5p ; hsa-mir-6737-5p ; hsa-mir-6793-5p ; hsa-mir-6742-5p ; hsa-mir-4472 ; hsa-mir-4447 ; hsa-mir-3151-5p ; hsa-mir-491-5p ; hsa-mir-6769b-5p ; hsa-mir-6769a-5p ; hsa-mir-6766-5p ; hsa-mir-6756-5p ; hsa-mir-6747-5p ; hsa-mir-608 ; hsa-mir-4651 ; hsa-mir-4664-5p ; hsa-mir-342-5p ; hsa-mir-6508-3p ; hsa-mir-4726-5p ; hsa-mir-4640-5p ; hsa-mir-202-3p ; 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-7a-5p ; hsa-mir-6823-3p ; hsa-mir-2114-3p ; hsa-mir-7162-3p ; hsa-mir-544b ; hsa-mir-299-3p ; hsa-mir-4293 ; hsa-mir-1273g-3p ; hsa-mir-141-5p ; hsa-mir-181a-2-3p ; hsa-mir-2682-3p ; hsa-mir-3691-3p ; hsa-mir-4436b-5p ; hsa-mir-4746-5p ; hsa-mir-6509-3p ; hsa-mir-6781-3p

Nearest miRNA

hsa-let-7i/Upstream/214929; hsa-mir-1178/Downstream/280696;

Nearest TSS

ENST00000382841/Upstream/2799; ENST00000547021/Downstream/829;

Nearest CpG islands

None/Target, chr12-CpG: 104/Upstream/100192, chr12-CpG: 204/Downstream/78670

Upstream sequence

tcccctcaaacttgctccatgtttcctctctctcttaccagtacatccattaagtcacttagttatcaaataaacctcaggctcatcccttaactAGGTG

Downstream sequence

accagataactattttaacaagctcttcaagatcttggattgctcaccgtgatataccaacacttggcTCCACAGAGCTTACTCTCAAAAGCATATTTTC

Target sequence

GTTACCAAATTCTCACAGTTGAACTATTTCAGTGCACTAACTGTTCTCTGTGTCTCAGCCAGTCCTCAATGCCCCAGGGTTTATTCACCCCATCTCCTTCCAACAGGGTGCTCTTTAGCATGACATGCCAAGTCCTTTAATGACCTCAGTTCCTACTATCAACTGCCACTGCTGCACCTGACACAGATCctgtgttccagacacatgcaacaaccagccctctcctgagctggccaaattttctcatagccatgc

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.