Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant in the Brassicaceae family and one of the principal model organisms in plant genetics, genomics, development, epigenetics, and molecular biology. Its compact genome, short generation time, extensive mutant collections, and well-developed community resources have made it a central reference species for functional plant research.
AraBase provides browser-based access to two major Arabidopsis reference resources. TAIR12 represents the current genome and annotation release used by AraBase, while TAIR10 together with Araport11 provides a widely used historical reference assembly and community annotation. These resources are presented separately to prevent ambiguity between assemblies and annotation releases.
This page summarizes the available genome assemblies, annotations, downloadable files, tools, external resources, and citation information. AraBase is developed and maintained by Heng Chen at the Department of Biology, University of Oxford, in his spare time. AraBase website content is licensed under CC BY-NC 4.0; commercial use requires separate permission.
Genome Information
| Metric | TAIR12 | TAIR10 |
|---|---|---|
| Genome size | 143.0 Mb | 119.7 Mb |
| Number of chromosomes | 7 | 7 |
| Scaffold L50 | 3 | 3 |
| Scaffold N50 | 27.8 Mb | 23.5 Mb |
| Number of genes | 26,867 | 27,562 |
| Number of transcripts | 36,573 | 48,265 |
| Number of TEs | 17,429 | 30,677 |
Main Data
| Resource | TAIR12 | TAIR10 / Araport11 |
|---|---|---|
| Genome assembly | Athaliana_TAIR12_genomic_Chr_softmasked.fa.gz | TAIR10_chr_all.fa.gz |
| Gene annotation | TAIR12_protein_coding_with_UTRs.gff3.gz | Araport11_GFF3_genes_transposons.20250813_protein_coding.gff3.gz |
| Non-coding RNA annotation | TAIR12_non_coding_RNA.gff3.gz | Araport11_GFF3_genes_transposons.20250813.gff3.all_ncRNAs.gff3.gz |
| TE annotation | TAIR12_All_TE.gff3.gz | Araport11_GFF3_genes_transposons.20250813_classified_transposable_element.gff3.gz |
| Complete annotation | TAIR12_genome_annotation_TAIR.gff3.gz | Araport11_GFF3_genes_transposons.20250813.gff3.gz |
News & Updates
View all newsThe AlphaFold based 3D structure prediction is now available.
AlphaFold based 3D structure prediction is now available for most proteins in Arabidopsis.
The gene expression atlas is update.
The ePlant/BAR gene expression atlas now supports multiple tissues, developmental stages, and more.
The new domain is available.
AraBase is now available from the updated Arabidopsis domain.
The gene expression of ePlant is integrated into the database!
Gene cards now connect Arabidopsis genes with ePlant expression views.
The TAIR10 is updated!
TAIR10 / Araport11 resources have been refreshed for comparison and legacy analyses.
Hello World! The AraBase is now available.
AraBase is available as a TAIR12-focused Arabidopsis genome database.
Citations
Please cite AraBase together with the relevant genome assembly, annotation release, and software used in your analysis.
AraBase
Chen, H., Emmerson, R., and Mosher, R. 2026. Near-gapless and haplotype-resolved Capsella genomes enable investigation into genomic consequences of mating system shifts. bioRxiv, 2026.07.10.737683. https://doi.org/10.64898/2026.07.10.737683
TAIR12
Reiser, L., Proia, A., Bakker, E., Subramaniam, S., Khosa, K., Sawant, S., Chen, X., Prithvi, T., and Berardini, T. Z. 2026. Recent major changes to TAIR: updates to the database, website, and Arabidopsis genome. Genetics 232(4):iyaf248. https://doi.org/10.1093/genetics/iyaf248
Wlodzimierz, P., Rabanal, F. A., Burns, R., et al. 2023. Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 618:557–565. https://doi.org/10.1038/s41586-023-06062-z
TAIR10
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia-Hernandez, M., Karthikeyan, A. S., Lee, C. H., Nelson, W. D., Ploetz, L., Singh, S., Wensel, A., and Huala, E. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40(D1):D1202–D1210. https://doi.org/10.1093/nar/gkr1090
Araport11
Cheng, C.-Y., Krishnakumar, V., Chan, A. P., Thibaud-Nissen, F., Schobel, S., and Town, C. D. 2017. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. The Plant Journal 89(4):789–804. https://doi.org/10.1111/tpj.13415
JBrowse 2
Diesh, C., Stevens, G. J., Xie, P., De Jesus Martinez, T., Hershberg, E. A., Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., Hogue, G., Wang, X., Liu, G., Dunn, M., Holmes, I. H., and Buels, R. M. 2023. JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology 24:74. https://doi.org/10.1186/s13059-023-02914-z
AlphaFold
Jumper, J., Evans, R., Pritzel, A., et al. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596:583-589. https://doi.org/10.1038/s41586-021-03819-2
UniProt
The UniProt Consortium. 2025. UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research 53(D1):D609-D617. https://doi.org/10.1093/nar/gkae1010
Gene Ontology
Ashburner, M., Ball, C., Blake, J., et al. 2000. Gene Ontology: tool for the unification of biology. Nature Genetics 25:25-29. https://doi.org/10.1038/75556
BAR / ePlant
Sullivan, A., Lombardo, M. N., Pasha, A., Lau, V., Zhuang, J. Y., Christendat, A., Pereira, B., Zhao, T., Li, Y., Wong, R., Qureshi, F. Z., and Provart, N. J. 2025. 20 years of the Bio-Analytic Resource for Plant Biology. Nucleic Acids Research 53(D1):D1576-D1586. https://doi.org/10.1093/nar/gkae920
