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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Plant Breeding and Biotechnology01:59

Plant Breeding and Biotechnology

Crop cultivation has a long history in human civilization, with records showing the cultivation of cereal plants beginning at around 8000 BC. This early plant breeding was developed primarily to provide a steady supply of food.
Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...

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Updated: May 28, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice

Yoshihiro Kawahara1, Tomoko Hirozane-Kishikawa2, Ryo Hirata3

  • 1Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, 305-8602, Japan. kawahara.yoshihiro177@naro.go.jp.

Rice (New York, N.Y.)
|May 27, 2026
PubMed
Summary
This summary is machine-generated.

The Rice Annotation Project Database (RAP-DB) enhances rice gene annotation using expert curation and AI, supporting molecular breeding. It now includes 1085 agronomically important loci and 1129 alleles, improving rice trait discovery.

Keywords:
Agronomically important genesAllelic variationArtificial intelligenceGene annotationGenome diversityLiterature-based manual curationRiceTranscriptome

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Last Updated: May 28, 2026

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08:09

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Published on: June 17, 2012

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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Area of Science:

  • Genomics
  • Plant Biology
  • Bioinformatics

Background:

  • High-throughput sequencing generates extensive rice genome data, but inferring gene function and traits remains complex.
  • The Rice Annotation Project Database (RAP-DB) is a vital resource for curated rice gene annotations.
  • Continuous updates based on scientific literature are crucial for maintaining genomic resource accuracy.

Purpose of the Study:

  • To update and expand the RAP-DB with comprehensive gene annotations and functional information for rice.
  • To integrate diverse datasets, including expression profiles and variation data, to support rice research.
  • To enhance the utility of RAP-DB for molecular breeding by cataloging agronomically important genes and alleles.

Main Methods:

  • Expert manual curation of peer-reviewed publications to update gene models and functional annotations.
  • Integration of community-curated datasets for key gene families (e.g., WRKY, RLKs, LRR).
  • Incorporation of RNA sequencing and microarray expression data, co-expression networks, and genome-wide variation data.
  • Implementation of AI-assisted literature screening and a user feedback system for continuous improvement.

Main Results:

  • As of February 2026, RAP-DB contains 7031 transcripts (6747 loci) curated from 4904 publications.
  • A catalog of 1085 agronomically important loci and 1129 functionally characterized alleles is now available.
  • Expanded coverage of regulatory and defense-related genes through community data integration.
  • Enhanced data visualization through integrated expression profiles and variation datasets.

Conclusions:

  • RAP-DB is strengthened as a primary, literature-based gene annotation resource for rice.
  • The database provides a practical foundation for molecular breeding and trait discovery in rice.
  • Continuous updates and community involvement ensure the long-term sustainability and accuracy of RAP-DB.