Basic Information
VIS ID
TVIS44005579
Fusion event
HTLV-1-RAPGEF2 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
chr4
Cytoband
q32.1
Reference genome
GRCh37/hg19
Start
160027807/159106655 (Hg38)
End
160027807/159106655 (Hg38)
Orient
+
Location type
Intronic
Target gene
RAPGEF2
miRNAs that regulate target gene
hsa-mir-335-5p ; hsa-mir-155-5p ; hsa-mir-1-3p ; hsa-mir-615-3p ; hsa-mir-149-5p ; hsa-mir-29b-2-5p ; hsa-mir-10a-5p ; hsa-mir-10b-5p ; hsa-mir-339-5p ; hsa-mir-659-3p ; hsa-mir-3620-3p ; hsa-mir-5002-5p ; hsa-mir-6748-3p ; hsa-mir-19a-3p ; hsa-mir-19b-3p ; hsa-mir-8066 ; hsa-mir-4720-5p ; hsa-mir-335-3p ; hsa-mir-3942-3p ; hsa-mir-7152-3p
Nearest miRNA
hsa-mir-12113/Upstream/6570139; hsa-mir-1305/Downstream/22147;
Nearest TSS
ENST00000502981/Upstream/2477; ENST00000503328/Downstream/121599;
Nearest CpG islands
None/Target, chr4-CpG: 46/Upstream/2672, chr4-CpG: 71/Downstream/4059654
Nearby gene
MIR3688-1(-22147) ;
Upstream sequence
TAAGCTTGATATCATGAACAGAAGGACAGGAATTAGGAAAGTTTTGCTGTTTTGCTTCCTTCTGTTTCTGAGGATAGACTCGATAAAGGAGTTTGCATGA
Downstream sequence
TTCTCGTTATAGGCAAAAGGAAAAGAATTGGGGAACATATGTAATTTTTTTTCCTGCTGTTCATTTCTGTTTGTTTTTTAAAGGCTTGCTGGCCTCATTC
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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