The TIGR Rice Genome Annotation project has continued to update and improve the rice genome sequence and annotation. In Release 4.0, 42,653 non-transposable element-related genes encoding 49,472 gene models were identified, with 13,237 genes related to transposable elements. The annotation was enhanced through the integration of multiple transcript and proteomic expression data sets, resulting in the annotation of 24,799 genes (31,739 gene models) as expressed in the rice genome. The Rice Genome Browser supports 59 tracks, providing detailed structural and functional annotations. Enhanced data access is available through web interfaces, FTP downloads, and a Data Extractor tool. The project also includes a Community Annotation initiative, where gene family experts contribute structural and functional annotations. Future improvements will focus on incorporating new transcript evidence and manually reviewing structural annotations. The high-quality, publicly accessible annotation of the rice genome is crucial for the interpretation of future cereal genome sequences.The TIGR Rice Genome Annotation project has continued to update and improve the rice genome sequence and annotation. In Release 4.0, 42,653 non-transposable element-related genes encoding 49,472 gene models were identified, with 13,237 genes related to transposable elements. The annotation was enhanced through the integration of multiple transcript and proteomic expression data sets, resulting in the annotation of 24,799 genes (31,739 gene models) as expressed in the rice genome. The Rice Genome Browser supports 59 tracks, providing detailed structural and functional annotations. Enhanced data access is available through web interfaces, FTP downloads, and a Data Extractor tool. The project also includes a Community Annotation initiative, where gene family experts contribute structural and functional annotations. Future improvements will focus on incorporating new transcript evidence and manually reviewing structural annotations. The high-quality, publicly accessible annotation of the rice genome is crucial for the interpretation of future cereal genome sequences.