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Oryza sativa

Oryza sativa

Arabidopsis thaliana

Arabidopsis thaliana

Zea mays

Zea mays

Solanum lycopersicum

Solanum lycopersicum

Hordeum vulgare

Hordeum vulgare


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
TotalBack-splicing site valided TotalSanger sequencing valided
Oryza sativa12,0371000405251Roots, shootsYe et al., 2015
2,35430007349LeavesLu et al., 2015
2,82402,824611410RootsYe et al., 2016
26,1603709585343Leaves, anthers, pistils, seeds, shoots, rootsThis study
Arabidopsis thaliana660000RootsWang et al., 2014
6,012000231188LeavesYe et al., 2015
16500054Siliques, seedsLu et al., 2015
970600106NASun et al., 2016
31,0791300822691Inflorescences, roots, leaves, aerialThis study
Zea mays49600011ShootsLu et al., 2015
Hordeum vulgare47160000Leaves and seedsDarbani et al. 2016
Solanum lycopersicum85400043FruitZuo 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
Oryza sativa40,31413770901539
Arabidopsis thaliana35,884250955792
Zea mays4960011
Hordeum vulgare4716000
Solanum lycopersicum8540043

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]

News:
    2017-01-24: PlantcircBase Release 1 online!
    2016-10-09: PlantcircBase beta version released!

References

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Search

Search

Search circRNAs in PlantcircBase.

View list

Browse

Browse all circRNAs in PlantcircBase.

Visualize

Visualize

Visualize structure of circRNAs.

BLASTcirc

Predict

Predict circRNAs from query sequences.

Download

Download

Download entries from PlantcircBase.

Help

Help

Manual of PlantcircBase.

Copyright©2017 Institute of Crop Sciences / Institute of Bioinformatics, Zhejiang University.
You are the NO.116020 visitor. Any questions or suggestions, please contact the Fan's lab, bioinplant@zju.edu.cn