R-loopAtlas

R-loopAtlas is a specialized database for R-loop (RNA-DNA hybrid) which contains experimental R-loop data mainly via the ssDRIP-seq method. Users can get R-loop information from Arabidopsis thaliana genome or another species genome to investigate some questions that relevant to R-loop. For details, please go to other pages on the website.


  1. The search function of R-loopAtlas.


    The section mainly realized two different search functions, including "searching R-loop by gene ID or gene symbol" and "searching R-loop by chromosome region". In "Search for R-loops by Gene" part, user can search R-loop information by gene ID or gene symbol (such as AT1G32580 or FLC).

    In "searching R-loop by chromosome region" part, user can search R-loop information by chromosome region coordinate.


  2. The browse function of R-loopAtlas.

    Firstly, the data of wide-genome R-loop of Arabidopsis thaliana was provided to the visitors in a table, including the start, end, and other information of detected R-loops by experiment.

    Secondly, plotted the genome-wide R-loop formation abundance profiles of Arabidopsis thaliana, which obtained from different time point of different conditions such as temperature, light, developmental stage, to provide researchers with a large R-loop abundance data matrix, which revealed the relationship among R-loop and stress, development stage and other.


  3. The BLAST function

    Using genome sequence, gene sequence and R-loop sequence to establish an alignment library, which could help researchers to determine the homologous relationship between the query sequence and the genome and genes in Arabidopsis, and make a simple prediction on whether the sequence is likely to form a R-loop structure.


  4. Other

    This section used JBrowse, a genome browser, to fulfill visualization of R-loop data. Matching genome and gene annotation with R-loop position in this module, which could show if R-loop was in the gene body, transcription start site, transcription termination site or intergenic region. This section also visualized R-loop abundance data using a chart-tool.
    R-loopAtlas realized the functions of storage, sharing and analysis of the R-loop data in plants and facilitate the biological research of R-loop in plants. We also will improve the functionality and practicability of the database to support R-loop research through continuous update and maintenance.