Pan-genome

• Rice RC - Rice Resource Center (10.1016/j.cell.2021.04.046)
• RPAN - RPAN: rice pan-genome browser for ~3000 rice genomes (10.1093/nar/gkw958)

Genome

• CRDC - China Rice Data Center
• Ensemble_Rice - Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species (10.1093/nar/gkx1011)
• IC4R - IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data (10.1016/j.gpb.2018.12.011)
• IRRI - International Rice Research Institute
• MBKbase - MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice (10.1093/nar/gkz921)
• Oryzabase - Oryzabase. An Integrated Biological and Genome Information Database for Rice (10.1104/pp.105.063008)
• OryzaGenome - OryzaGenome: Genome Diversity Database of Wild Oryza Species (10.1093/pcp/pcv171)
• RAP-DB - Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics (10.1093/pcp/pcs183)
• RGAP - Rice Genome Annotation Project
• RiceRelativesGD - RiceRelativesGD: a genomic database of rice relatives for rice research (10.1093/database/baz110)
• RIGW - Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes (10.1016/j.molp.2017.10.003)

Functional Gene

• funRiceGenes - funRiceGenes dataset for comprehensive understanding and application of rice functional genes (10.1093/gigascience/gix119)
• OGRO - OGRO: The Overview of functionally characterized Genes in Rice Online database (10.1186/1939-8433-5-26)

Variation

• HapRice - HapRice, an SNP Haplotype Database and a Web Tool for Rice (10.1093/pcp/pct188)
• Rice Diversity - Rice Diversity
• RiceNavi - A quantitative genomics map of rice provides genetic insights and guides breeding (10.1038/s41588-020-00769-9)
• Rice SNP-Seek Database - SNP-Seek database of SNPs derived from 3000 rice genomes; Rice SNP-seek database update: new SNPs, indels, and queries (10.1093/nar/gkw1135)
• RiceVarMap - RiceVarMap: a comprehensive database of rice genomic variations; An inferred functional impact map of genetic variants in rice (10.1016/j.molp.2021.06.025)
• SR4R - SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice (10.1016/j.gpb.2020.03.002)

Transcriptome & Epigenome

• ARMOUR - ARMOUR – A Rice miRNA: mRNA Interaction Resource (10.3389/fpls.2018.00602)
• CREP - A dynamic gene expression atlas covering the entire life cycle of rice (10.1111/j.1365-313X.2009.04100.x)
• eRice - eRice: a refined epigenomic platform for japonica and indica rice (10.1111/pbi.13329)
• OryzaExpress - PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data (10.1093/pcp/pcw208)
• RED - Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice (10.1016/j.jgg.2017.05.003)
• RiceENCODE - RiceENCODE: A comprehensive epigenomic database as a rice Encyclopedia of DNA Elements (10.1016/j.molp.2021.08.018)
• RiceFREND - RiceFREND: a platform for retrieving coexpressed gene networks in rice (10.1093/nar/gks1122)
• RiceGE - Rice Functional Genomic Express Database
• RiceLncPedia - RiceLncPedia: a comprehensive database of rice long non-coding RNAs (10.1111/pbi.13639)
• Rice MPSS database - Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA (10.1093/nar/gkj077)
• RiceXPro - RiceXPro version 3.0: expanding the informatics resource for rice transcriptome (10.1093/nar/gks1125)
• TENOR - TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice (10.1093/pcp/pcv179)

Others

• OryGenesDB - OryGenesDB: a database for rice reverse genetics (10.1093/nar/gkj012)
• RECoN - RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response (10.3389/fpls.2017.01640)
• RFGB - Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0 (10.1111/pbi.13215)
• RiceAntherNet - RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes (10.1111/tpj.13744)
• Ricebase - Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data (10.1093/database/baw107)
• RiceCye - Rice Metabolic Pathways
• RiceMetaSysB - RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes (10.1093/database/baz015)
• RiceNet - RiceNet v2: an improved network prioritization server for rice genes (10.1093/nar/gkv253)
• RiceWiki - RiceWiki: a wiki-based database for community curation of rice genes (10.1093/nar/gkt926)
• RiTE-db - RiTE database: a resource database for genus-wide rice genomics and evolutionary biology (10.1186/s12864-015-1762-3)
• RKD - Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes (10.1186/s12284-016-0106-5)
• RMD - RMD: a rice mutant database for functional analysis of the rice genome (10.1093/nar/gkj016)
• RMOS - Rice Microarray Opening Site
• RSIADB - RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA (10.1093/database/baw031)
• RTFDB - A web-based tool for the prediction of rice transcription factor function (10.1093/database/baz061)
• RTIMD - Rice Tos17 Insertion Mutant Database
• SemanticGO - SemanticGO: a tool for gene functional similarity analysis in Arabidopsis thaliana and rice (10.1016/j.plantsci.2020.110527)
• ThRSDB - ThRSDB: a database of Thai rice starch composition, molecular structure and functionality (10.1093/database/baaa068)

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