Basic Information
VIS ID
TVIS44005296
Fusion event
HTLV-1-GPATCH3 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
chr1
Cytoband
p36.11
Reference genome
GRCh37/hg19
Start
27224360/26897869 (Hg38)
End
27224360/26897869 (Hg38)
Orient
+
Location type
Intronic
Fragile sites / regions
FRA1A
Target gene
GPATCH3
miRNAs that regulate target gene
hsa-mir-339-5p ; hsa-mir-6848-5p ; hsa-mir-6846-5p ; hsa-mir-6825-5p ; hsa-mir-3191-3p ; hsa-mir-6883-5p ; hsa-mir-6785-5p ; hsa-mir-149-3p ; hsa-mir-4728-5p ; hsa-mir-92b-5p ; hsa-mir-6805-5p ; hsa-mir-1184 ; hsa-mir-1205 ; hsa-mir-1286 ; hsa-mir-1305 ; hsa-mir-148a-5p ; hsa-mir-148b-5p ; hsa-mir-17-3p ; hsa-mir-208a-5p ; hsa-mir-208b-5p ; hsa-mir-3158-5p ; hsa-mir-3973 ; hsa-mir-4459 ; hsa-mir-4695-5p ; hsa-mir-4722-5p ; hsa-mir-520g-3p ; hsa-mir-520h ; hsa-mir-544a ; hsa-mir-607 ; hsa-mir-6874-3p ; hsa-mir-873-5p
Nearest miRNA
hsa-mir-12136/Upstream/343276; hsa-mir-101-1/Downstream/3841287;
Nearest TSS
ENST00000473358/Upstream/4421; ENST00000435827/Downstream/2369;
Nearest CpG islands
None/Target, chr1-CpG: 111/Upstream/7315, chr1-CpG: 45/Downstream/2132
Upstream sequence
GCAACACTTGAGCCAGAAATTGGCCAATGTTTAAATCTGTTAGCCTTTCCCTAGTAAACATCTAGTAAATCCCTAGTAAAAATCTAggccgacacagtgg
Downstream sequence
ctcacgcttgtgatcccagcactttgggaggctgaggcaggaggattgcttgagctcaggagttcaagaccagcctgggcaaaatggtgagacccttatc
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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