Welcome to Plant circular RNA Database (PlantcircBase)!
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 eukaryotes (Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013), including plants (Wang et al. 2014, Ye et al. 2015, Lu et al. 2015).
In PlantcircBase (http://ibi.zju.edu.cn/plantcircbase/), we collected publicly available back-splice junction sequences and their full-length sequences of circRNAs identified in plants by us and other groups (Table 1). Based on the collected circRNAs, we further predicted those circRNAs putatively acting as miRNA sponges and their potential networks involving circRNA-miRNA-mRNA in the corresponding species. In the database, you can find plant circRNAs and their related information, such as their sequences, host genes, expression, experimental validation as well as bioinformatics tools for visualizing circRNA structures and predicting circRNAs from query sequences.
Table 1 The number of circRNAs in PlantcircBase (Release 1)
|Organisms||Number of circRNAs||Full-length sequence of circRNAs||Acting as miRNA sponge*||Networks of circRNA-miRNA-mRNA*||Tissues||References|
|Total||Back-splicing site valided||Total||Sanger sequencing valided|
|Oryza sativa||12,037||10||0||0||405||251||Roots, shoots||Ye et al., 2015|
|2,354||30||0||0||73||49||Leaves||Lu et al., 2015|
|2,824||0||2,824||61||14||10||Roots||Ye et al., 2016|
|26,160||37||0||9||585||343||Leaves, anthers, pistils, seeds, shoots, roots||This study|
|Arabidopsis thaliana||6||6||0||0||0||0||Roots||Wang et al., 2014|
|6,012||0||0||0||231||188||Leaves||Ye et al., 2015|
|165||0||0||0||5||4||Siliques, seeds||Lu et al., 2015|
|970||6||0||0||10||6||NA||Sun et al., 2016|
|31,079||13||0||0||822||691||Inflorescences, roots, leaves, aerial||This study|
|Zea mays||496||0||0||0||1||1||Shoots||Lu et al., 2015|
|Hordeum vulgare||47||16||0||0||0||0||Leaves and seeds||Darbani et al. 2016|
|Solanum lycopersicum||854||0||0||0||4||3||Fruit||Zuo et al. 2016|
Table 2 Summary of circRNA entries in PlantcircBase (Release 1)
|Organisms||Total circRNAs||Back-splicing site validated||Full length sequence validated||Acting as miRNA sponge||Networks of circRNA-miRNA-mRNA|
How to cite this database:
Qinjie Chu, Xingchen Zhang, Xintian Zhu, Chen Liu, Lingfeng Mao, Chuyu Ye, Qianhao Zhu, Longjiang Fan. 2017. PlantcircBase: a database for plant circular RNAs. Molecular Plant [Full text]
2017-01-24: PlantcircBase Release 1 online!
2016-10-09: PlantcircBase beta version released!