PlantCRE is a deep learning-based web server which has learned the cis-regulatory code of plant genes from four plant species of Arabidopsis, Zea mays, Oryza sativa and Solanum lycopersicum.
As an application, it can identify plant cis-regulatory elements (CREs) of given gene(s), as well as locate the exact position of each CRE.
Citation: Yang Qiu#, Lifen Liu#, Jiali Yan#, Xianglei Xiang, Shouzhe Wang, Yun Luo, Kaixuan Deng, Jieting Xu, Minliang Jin, Xiaoyu Wu, Liwei Cheng, Ying Zhou, Weibo Xie, Hai-Jun Liu, Alisdair R. Fernie, Xuehai Hu* and Jianbing Yan*.
Precise engineering of gene expression by editing plasticity.
Model: Genome-wide CREs identifier for Solanum lycopersicum
Enter a Gene or Gene list:
(Please use spaces to separate multiple genes, up to a maximum of 10 genes.)
Model introduction
This basenji2 model was trained on a large-scale dataset containing 34,725 Solanum lycopersicum genes. Its input is genome sequences of length 90kb, which include 70kb upstream and 20kb downstream of the TSS. Its output is the maximal expression level across 55 RNA-seq experiments.
our website is a powerful tool for identifying cis-regulatory elements for genes, it help plant scientists to clearly find the exact position of each CRE.