MEPDB: Database of microExons in plants.

Yakub Islamov, Huihui Yu, Hongfeng Yu, Chi Zhang

Abstract read

In one paragraph

Article in The New phytologist, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing 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

1 citing paper in PubMed.

MEPDB: Database of microExons in plants.The New phytologist · 2025
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

4 authors.

Yakub Islamov *Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA.

Huihui Yu *Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.ORCID https://orcid.org/0000-0003-2725-1937

Hongfeng YuSchool of Computing, University of Nebraska, Lincoln, NE, 68583, USA.ORCID https://orcid.org/0000-0002-0596-8227

Chi ZhangSchool of Biological Sciences, Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.ORCID https://orcid.org/0000-0002-1827-8137

Funding

National Natural Science Foundation of China 32470237Nebraska Soybean Board #725US Department of Energy DE-SC0024337

6 · The paper itself

Abstract

Microexons, ≤ 51-nucleotide (nt), particularly ultra-short ones (1-15 nt), are challenging to identify due to their small size and frequent absence in genome annotations, which limits understanding of their biological roles. Using our developed pipeline, we identified 2398 small internal microexons across 10 diverse plant species, and most of them were not annotated in the reference genomes. These microexons are grouped into 45 conserved microexon clusters based on microexon-tags, which include the coding microexons and portions of flanking exon sequences. Leveraging these clusters, we developed a predictive method that identified 20 224 microexons across 132 plant genomes. For these microexons, we developed the Database of MicroExons in Plants (MEPDB), which includes genomic coordinates, sequences (nucleotide/amino acid), gene annotations, and updated CDS information for microexon annotations, as well as an integrated tool for RNA-seq-independent microexon prediction, thereby offering a comprehensive resource for plant microexon research.

Indexed as

Databases, GeneticExonsPlantsGenome, PlantMolecular Sequence Annotationgene structure annotationmicroexon predictionmicroexonsmicroexon‐tagsplant genomes

Identifiers

PMID40817693

DOI10.1111/nph.70456

PMCPMC12409088

What OpenQuestion holds

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LicenceCC BY

Read underepoch 390

Registered trials

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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.