Docs
AraBase documentation will explain how to use the TAIR12 database, interpret download files, cite releases, and move between locus search, sequence extraction, and genome browser views.
Documentation Sections
| Section | Status | Notes |
|---|---|---|
| Quick start | TBD | Basic navigation, search examples, and browser examples. |
| Identifier guide | TBD | TAIR12 gene, transcript, TE, repeat, and chromosome naming conventions. |
| File formats | TBD | FASTA, GFF3/GTF, BED, BigWig/BigBed, and tabular annotation files. |
| Tool guide | TBD | Locus Search, Sequence Extract, and Genome Browser usage notes. |
| Release and citation policy | TBD | Versioning, checksums, data provenance, and citation wording. |
Coordinate System
All AraBase coordinates should be interpreted against the TAIR12 genome assembly unless otherwise stated. Coordinate-base conventions, interval inclusivity, and strand behavior are TBD and should be documented before public data release.
Search Locus And Gene Cards
Use Search Locus to open static AraBase gene cards. Select
TAIR12 or TAIR10 / Araport11, enter a gene or transcript ID such as AT1G01010,
and submit the search. Direct links can also pass both query parameters, for
example /tools/search-locus/?release=TAIR12&id=AT1G01010.
Gene cards show locus coordinates, release, strand, feature type, transcripts, protein products where annotated, available functional descriptions and aliases, external TAIR/ePlant links where they can be generated safely, a lazy-loaded AtGenExpress eFP expression map, and an embedded JBrowse view focused on the locus. Transcript, CDS, protein, and gene sequence copy actions reuse the AraBase Sequence Extract static stores.
Use the release selector to keep TAIR12 and TAIR10 / Araport11 records separate. The current search implementation is strongest for gene and transcript IDs; it does not yet claim complete keyword, GO-term, or external identifier search. Homolog information is not provided on this page.
AtGenExpress eFP
The AtGenExpress eFP panel displays a developmental expression map generated by the Bio-Analytic Resource for Plant Biology.
The panel is collapsed by default and the image is requested only after the user opens it. The selected AGI gene ID is passed to the BAR eFP image API using the Developmental Map in Absolute mode.
Expression data are maintained independently of the selected TAIR12 or TAIR10 genome annotation release. Users can also open the full-size expression map or the complete ePlant gene view in a new tab. This feature depends on BAR service availability.
Citation
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
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