Evidence map›Paper›PMID 35637632›Full record

ArticlePlant communications2022

PlantcircBase 7.0: Full-length transcripts and conservation of plant circRNAs.

Xiaoxu Xu, Tianyu Du, Weihua Mao, Xiaohan Li, Chu-Yu Ye, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Overview of circular RNA databases and other resources.Nature reviews. Molecular cell biology · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Online Databases in Circular RNAs.Advances in experimental medicine and biology · 2025
    Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Review
  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Xiaoxu XuInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China.
Tianyu DuInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China.
Weihua MaoAnalysis Center of Agrobiology and Environmental Science, Zhejiang University, Hangzhou 310058, China.
Xiaohan LiInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
Chu-Yu YeInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
Qian-Hao ZhuCSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, ACT 2601, Australia.
Longjiang FanInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China.
Qinjie ChuInstitute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China. Electronic address: qinjiechu@zju.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Circular RNA (circRNA) is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants. Five years ago, we developed a comprehensive plant circRNA database (PlantcircBase), which has attracted much attention from the plant circRNA community. Here, we report an updated PlantcircBase (v.7.0), which contains 171,118 circRNAs from 21 plant species. Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing (RNA-seq) datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study. A plant multiple conservation score (PMCS), based on the conservation of both sequence and expression profiles, was calculated for each circRNA to quantify and compare the conservation of all circRNAs. A new parameter, plant circRNA confidence level (PCCL), is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA. All this information and other details of circRNAs can be browsed, searched, and downloaded from PlantcircBase 7.0, which also provides online bioinformatics tools for visualization and sequence alignment. PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.

Indexed as

Databases, Nucleic AcidRNA, CircularPlantsReproducibility of ResultsRNA, PlantSequence Analysis, RNARNA, CircularRNA, Plantconservationfull-length transcriptslong-read sequencingPlantcircBaseplant circRNA

Identifiers

PMID35637632
PMCPMC9284285

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.