Basic Information
VIS ID
TVIS44011050
Fusion event
HTLV-1-SHCBP1 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
chr16
Cytoband
q11.2
Reference genome
GRCh37/hg19
Start
46615817/46581905 (Hg38)
End
46615817/46581905 (Hg38)
Orient
-
Location type
Exonic
Target gene
SHCBP1
miRNAs that regulate target gene
hsa-mir-193b-3p ; hsa-mir-425-5p ; hsa-mir-340-5p ; hsa-mir-33a-5p ; hsa-mir-32-5p ; hsa-mir-19b-3p ; hsa-mir-877-3p ; hsa-mir-455-3p ; hsa-mir-200b-3p ; hsa-mir-200c-3p ; hsa-mir-429 ; hsa-mir-580-3p ; hsa-mir-7153-5p ; hsa-mir-146b-5p ; hsa-mir-146a-5p ; hsa-mir-589-5p ; hsa-mir-4433a-3p ; hsa-mir-4459 ; hsa-mir-4768-3p ; hsa-mir-6500-3p ; hsa-mir-3614-5p ; hsa-mir-4773 ; hsa-mir-2115-3p ; hsa-mir-5003-3p ; hsa-mir-1183 ; hsa-mir-34a-3p ; hsa-mir-19a-3p
Nearest miRNA
hsa-mir-1225/Upstream/12418232; hsa-mir-11401/Downstream/3710711;
Nearest TSS
ENST00000527434/Upstream/10795018; ENST00000569239/Downstream/2348;
Nearest CpG islands
None/Target, chr16-CpG: 29/Upstream/152931, chr16-CpG: 42/Downstream/39185
Upstream sequence
GTGACATTAAGTTGTCATCAGCTTGCGTGATCCCCAGTTCACTCAACCTTTTCTTCTTTATCTGGCCTTTCTGTGTGGAGGCAGCAATTAGTTCATTTAC
Downstream sequence
AATTTCACAATTTCCCTCGACTTGCTCAGAAGGGTCAGTTCTTGCACAAAGCTCCATTTTACCAGTTGCACACTCAATCAGCTCTTCTAGATCCACTCTT
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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