Manual of VirusCircBase

  1. Instructions
  2. Detail information of an entry
  3. miRNA
  4. Submit your data
  5. About us

Intructions

Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. Typical circular RNA molecules comprise canonically spliced exonic sequences and are covalently closed. They have recently been shown to be expressed in microbiology, including virus.

In VirusCircBase, we firstly obtained 56 datasets from NCBI SRA database which searched by the keyword of "virus" and screened by some other keywords such as "rRNA-depleted", "RNase R" and "polyA-RNA depleted" . Then, the circRNAs were identified with three tools : CIRI2, find_circ, circRNA_finder. In total,we detected 46,400 circRNAs in 26 viruses from 15 viral families. The circRNAs and their related information , including location , expression , sources , were provided in the database.

Detail information of an entry

For each entry in VirusCircBase, a list of items have been displayed. The table below describes the detailed meaning of each item.

circRNA name

In our naming system , each circRNA have an unique number in our database, an abbreviation for the corresponding virus and the host infected by virus. Finally,the three parts were connected with '_circ_'.

Viralgenome

The accession number of the reference genome used in VirusCircBase.

Start

Start site of the circRNA in reference sequence.

End

End site of the circRNA in reference sequence.

Strand

Strand information.

Gene

The virus genes in which the circRNA is involved .

Junction read counts

CircRNA junction read counts.( The total number of reads that support the junction of the circRNA. )

Detection tool

Bioinformatics tools used to identify circRNA.

Host

Host of the virus.

Cell/tissue

Cell or tissue infected by the virus

Virus name

Name of the virus

Virus taxid

ID of the virus in NCBI Taxonomy database

Genomic length

Genomic length of the viral genome

GEO

NCBI SRA or GEO information corresponding to the dataset.

Sample

The sample information corresponding to the SRA dataset.

PMID

The paper in which the circRNA was verified by experiments.

miRNA

Potential interaction between miRNAs and circRNAs were predicted using TarPmiR. For each circRNA, the miRNAs which may interact with the circRNA were provided . Besides , the interaction probability and interaction region were also provided.

Submit your data

If you would like to submit your data to VirusCircBase, or to suggest implementation of a published circRNA dataset, please contact us by Email : pys2013@hnu.edu.cn

About us

VirusCircBase is developed by the Peng lab in College of Biology, Hunan University, Changsha, China .
Email: pys2013 AT hnu.edu.cn