Basic Information
VIS ID
TVIS44007166
Fusion event
HTLV-1-RARB integration
Validated
No
Detection method
HTS
Data source
download(RID)
Sample type
Nontumor
Disease
Adult T-cell leukemia (ATL)
Quality evaluation
Normal
Reported year
2014
PubMed ID
24735963
Virus Sequence
Virus name
HTLV-1
Reference genome
Not given
Host Sequence
Chromosome
chr3
Cytoband
p24.2
Reference genome
GRCh37/hg19
Start
25007567/24966076 (Hg38)
End
25007567/24966076 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA3A
Target gene
RARB
miRNAs that regulate target gene
hsa-mir-16-2-3p ; hsa-mir-30c-5p ; hsa-mir-15a-5p ; hsa-mir-16-5p ; hsa-mir-33a-3p ; hsa-mir-15b-5p ; hsa-mir-195-5p ; hsa-mir-424-5p ; hsa-mir-497-5p ; hsa-mir-545-5p ; hsa-mir-4307 ; hsa-mir-6792-5p ; hsa-mir-6838-5p ; hsa-let-7c-5p ; hsa-mir-548c-3p ; hsa-mir-548x-3p ; hsa-mir-548j-3p ; hsa-mir-548aq-3p ; hsa-mir-548am-3p ; hsa-mir-548aj-3p ; hsa-mir-548ah-3p ; hsa-mir-548ae-3p ; hsa-mir-578 ; hsa-mir-1-3p ; hsa-mir-106a-5p ; hsa-mir-146a-5p ; hsa-mir-146b-5p
Nearest miRNA
hsa-mir-12127/Upstream/4828435; hsa-let-7g/Downstream/698797;
Nearest TSS
ENST00000440867/Upstream/278157; ENST00000489694/Downstream/208256;
Nearest CpG islands
None/Target, chr3-CpG: 148/Upstream/135476, chr3-CpG: 125/Downstream/697989
Nearby gene
RARB(+208256) ;
Nearest cancer related gene
RARB(TSG, No orient, 0)
Upstream sequence
AAAATATGCAGGTTTACATGGAAAGTCACATTGGCCTGGTTAGCCTTATTAAAGTAAATAAGTTGGGAAACATATTCAGAAAGTTTAGAAATGCAACTAA
Downstream sequence
AGAGGCACCTTTATCTTTGAATTTTTTTTTTTTTTGGTTATTTTAGCTTGTTAAATTATTTTTCTTTGGCACTGACCTTTGGCATTTTTACTACTTGATT
Reference
Cook, L. B., et al. The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma. Blood,2014, 123(25): 3925-3931.
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