VISDB - VIS Detail

Expression analysis of TCGA samples

Basic Information

VIS ID

TVIS10016445

Fusion event

HBV-GRIN2A integration

Validated

No

Detection method

WGS

Data source

Curated

Sample type

Tumor

Disease

Hepatocellular carcinoma (HCC)

Quality evaluation

Good

Reported year

2012

PubMed ID

22267523

Virus Sequence

Virus name

HBV

Reference genome

NC_003977

Start

2991

End

3026

Orient

+

Integrated sequence

GAGCTGGAGCATTCGGGCTGGGTTTCACCCCACCGC

Host Sequence

Chromosome

chr16

Cytoband

p13.2

Reference genome

GRCh37/hg19

Start

9953813/9859956 (Hg38)

End

9953848/9859991 (Hg38)

Orient

-

Location type

Intronic

Target gene

GRIN2A

miRNAs that regulate target gene

hsa-mir-125b-5p ; hsa-mir-3915 ; hsa-mir-4710 ; hsa-mir-657 ; hsa-mir-3679-5p ; hsa-mir-3665 ; hsa-mir-1185-5p ; hsa-mir-3928-3p ; hsa-mir-125a-3p ; hsa-mir-583 ; hsa-mir-192-3p ; hsa-mir-6806-5p ; hsa-mir-5189-3p ; hsa-mir-4482-5p ; hsa-mir-3130-5p ; hsa-mir-1912 ; hsa-mir-1295b-5p ; hsa-mir-5589-3p ; hsa-mir-216a-5p ; hsa-mir-216b-5p ; hsa-mir-4753-3p ; hsa-mir-130b-5p ; hsa-mir-616-5p ; hsa-mir-373-5p ; hsa-mir-371b-5p ; hsa-mir-6769b-3p ; hsa-mir-4723-3p ; hsa-mir-3183 ; hsa-mir-6840-3p ; hsa-mir-873-5p ; hsa-mir-1228-3p ; hsa-mir-3914 ; hsa-mir-6800-3p ; hsa-mir-1276 ; hsa-mir-519e-5p ; hsa-mir-515-5p ; hsa-mir-3941 ; hsa-mir-2355-5p ; hsa-mir-136-5p ; hsa-mir-603 ; hsa-mir-362-3p ; hsa-mir-8485 ; hsa-mir-329-3p ; hsa-mir-148a-5p ; hsa-mir-3123 ; hsa-mir-3154 ; hsa-mir-3925-5p ; hsa-mir-411-5p ; hsa-mir-5010-3p ; hsa-mir-6770-5p ; hsa-mir-6832-5p ; hsa-mir-7515

Nearest miRNA

hsa-mir-1225/Upstream/4227390; hsa-mir-11401/Downstream/1446449;

Nearest TSS

ENST00000527434/Upstream/65319; ENST00000569218/Downstream/78567;

Nearest CpG islands

None/Target, chr16-CpG: 29/Upstream/767124, chr16-CpG: 282/Downstream/320095

Nearest cancer related gene

GRIN2A(TSG, No orient, 0)

Upstream sequence

atgttgcaaatttgacagatttatatgaaaaattatggtctctctggaatttaaatttaagtaggagtGTGGCAACTCTAGATGTGGGGAGATGCAAGTT

Downstream sequence

tatcctatccctagagtttccagtctcggtggagagaagtcaaagcttaatagcaatgaagtgaatgaagtgagacaaatgctatgccgggagcaggcac

Target sequence

tggggctacggtggtgaacagtcctcagagaggtc

Reference

Jiang, S., et al. Re-evaluation of the carcinogenic significance of hepatitis B virus integration in hepatocarcinogenesis. PLoS One ,2012, 7(9): e40363.