The TIGR Rice Genome Annotation Resource has been updated to Release 4.0, incorporating new data and improving annotation quality. The project has identified 42,653 non-transposable element-related genes and 49,472 gene models due to alternative splicing detection. Additionally, 13,237 genes related to transposable elements were identified through refined methods. With the integration of transcript and proteomic data, 24,799 genes (31,739 gene models) were annotated, representing approximately 50% of all gene models. The Rice Genome Browser now supports 59 tracks and provides enhanced data access through web interfaces, FTP, and a Data Extractor tool. The project has improved the rice genome annotation by using pseudomolecule-level annotation, which streamlines computational processes and reduces physical gaps in the genome. In Release 4, three major modifications were implemented to enhance gene model quality. These include using PASA for spliced alignments at the pseudomolecule level, eliminating duplicated regions between BAC/PAC clones, and implementing a manual review process that accepted 87% of the proposed gene models. The project also updated the TIGR Oryza Repeat Database with 201 new rice repetitive sequences and improved automated function assignment using Pfam domain annotations. Expression data, including ESTs, full-length cDNAs, MPSS, SAGE, and proteomic data, were integrated to enhance gene model functional annotation. The Rice Genome Browser now displays structural, functional, and comparative annotations, including Transcript Assemblies instead of Gene Indices for transcript support. The project also mapped probes from five publicly available rice microarray platforms to the genome, updating the Generic Genome Browser to version 1.64 and upgrading the Gbrowse server to MySQL 5. Segmental duplication analysis was conducted, identifying duplicated blocks in the rice genome. A Community Annotation project was initiated, allowing gene family experts to contribute structural and functional annotations. The project has released 454 genes with Community Annotation and is in the process of validating another 142 genes. Data from the project are available through web interfaces, FTP, and a Data Extractor tool. Release 5 is currently being prepared, incorporating approximately 780,000 ESTs from GenBank as new transcript evidence. The project aims to provide high-quality, publicly accessible annotation for the rice genome, serving as a major resource for cereal genome sequencing and annotation.The TIGR Rice Genome Annotation Resource has been updated to Release 4.0, incorporating new data and improving annotation quality. The project has identified 42,653 non-transposable element-related genes and 49,472 gene models due to alternative splicing detection. Additionally, 13,237 genes related to transposable elements were identified through refined methods. With the integration of transcript and proteomic data, 24,799 genes (31,739 gene models) were annotated, representing approximately 50% of all gene models. The Rice Genome Browser now supports 59 tracks and provides enhanced data access through web interfaces, FTP, and a Data Extractor tool. The project has improved the rice genome annotation by using pseudomolecule-level annotation, which streamlines computational processes and reduces physical gaps in the genome. In Release 4, three major modifications were implemented to enhance gene model quality. These include using PASA for spliced alignments at the pseudomolecule level, eliminating duplicated regions between BAC/PAC clones, and implementing a manual review process that accepted 87% of the proposed gene models. The project also updated the TIGR Oryza Repeat Database with 201 new rice repetitive sequences and improved automated function assignment using Pfam domain annotations. Expression data, including ESTs, full-length cDNAs, MPSS, SAGE, and proteomic data, were integrated to enhance gene model functional annotation. The Rice Genome Browser now displays structural, functional, and comparative annotations, including Transcript Assemblies instead of Gene Indices for transcript support. The project also mapped probes from five publicly available rice microarray platforms to the genome, updating the Generic Genome Browser to version 1.64 and upgrading the Gbrowse server to MySQL 5. Segmental duplication analysis was conducted, identifying duplicated blocks in the rice genome. A Community Annotation project was initiated, allowing gene family experts to contribute structural and functional annotations. The project has released 454 genes with Community Annotation and is in the process of validating another 142 genes. Data from the project are available through web interfaces, FTP, and a Data Extractor tool. Release 5 is currently being prepared, incorporating approximately 780,000 ESTs from GenBank as new transcript evidence. The project aims to provide high-quality, publicly accessible annotation for the rice genome, serving as a major resource for cereal genome sequencing and annotation.