VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10019692

Fusion event

HBV-CPS1 integration

Validated

No

Detection method

VirusFinder

Data source

Curated

Sample type

Nontumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Normal

Reported year

2017

PubMed ID

28622513

Virus Sequence

Virus name

HBV

Reference genome

NC_003977

Start

1825

Integrated sequence

TAAAGACTGGGAGGAGTTGGGGGAGGAGATTAGGTTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTT| |TTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATCGACCCTTATAAAGA

Host Sequence

Chromosome

chr2

Cytoband

q34

Reference genome

GRCh37/hg19

Start

211421667/210556943 (Hg38)

End

211421667/210556943 (Hg38)

Location type

Intron2

Target gene

CPS1

miRNAs that regulate target gene

hsa-mir-17-5p ; hsa-mir-3121-3p ; hsa-mir-4255 ; hsa-mir-4709-3p ; hsa-mir-7154-5p ; hsa-mir-101-3p ; hsa-mir-1255b-5p ; hsa-mir-1255a ; hsa-mir-6744-5p ; hsa-mir-8060 ; hsa-mir-16-1-3p ; hsa-mir-144-3p ; hsa-mir-216a-5p ; hsa-mir-522-3p ; hsa-mir-224-3p ; hsa-mir-4694-3p ; hsa-mir-6516-5p ; hsa-mir-6738-3p ; hsa-mir-1303 ; hsa-mir-3678-3p ; hsa-mir-1273h-3p ; hsa-mir-5001-3p ; hsa-mir-4727-5p ; hsa-mir-1200 ; hsa-mir-142-3p ; hsa-mir-630 ; hsa-mir-146b-3p ; hsa-mir-6799-3p ; hsa-mir-3173-5p ; hsa-mir-7976 ; hsa-mir-496 ; hsa-mir-302a-5p ; hsa-mir-18a-3p ; hsa-mir-324-3p ; hsa-mir-1913 ; hsa-mir-4682 ; hsa-mir-544b ; hsa-mir-4324 ; hsa-mir-4778-5p ; hsa-mir-200b-5p ; hsa-mir-200a-5p ; hsa-mir-4796-3p ; hsa-mir-93-5p ; hsa-mir-526b-3p ; hsa-mir-519d-3p ; hsa-mir-20b-5p ; hsa-mir-20a-5p ; hsa-mir-106b-5p ; hsa-mir-106a-5p ; hsa-mir-548ah-5p ; hsa-mir-3609 ; hsa-mir-548l ; hsa-mir-8054 ; hsa-mir-548k ; hsa-mir-548av-5p ; hsa-mir-548c-3p

Nearest miRNA

hsa-mir-10b/Upstream/2802062; hsa-mir-1244-1/Downstream/1869320;

Nearest TSS

ENST00000437798/Upstream/209; ENST00000497163/Downstream/20212;

Nearest CpG islands

None/Target, chr2-CpG: 135/Upstream/80131, chr2-CpG: 86/Downstream/1980513

Upstream sequence

aattctgacacaagctaccacatggataaaccctcaaagacactgtgctaagtgaaataaaccagacataaaaggacaaagattggccaggcttggtggc

Downstream sequence

ACAGTTTTGAATGTAGCTCTGAAGTACTAATGTATTAATGTTTCCTTTACTGTGGAACCTACTGACTTAGCAAATGCTAATTTTTATCTTATCTGAGTAA

Reference

Cancer Genome Atlas Research Network. Electronic address, w. b. e. and N. Cancer Genome Atlas Research . Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell ,2017,169(7): 1327-1341 e13