ArticleNucleic acids research2012
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 209 papers.
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209 citing papers in PubMed.
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- Evolution of Repetitive Genomic Content and Gene Families Over Geo-Climatic Gradients in Brassicaceae.Ecology and evolution · 2025Article
- PIF4-dependent 2-hydroxymelatonin and 3-hydroxymelatonin biosynthesis is involved in skotomorphogenic seedling growth in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2025Article
- T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.Genome biology · 2025Article
- Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4.BMC plant biology · 2025Article
- A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation.Developmental cell · 2025Article
- Analysis of xyloglucan metabolism mutants highlights the prominent role of xylose cleavage in seed dormancy.The Plant journal : for cell and molecular biology · 2025Article
- The transcription factor NF-YA10 determines the area explored by Arabidopsis thaliana roots and directly regulates LAZY genes.The Plant journal : for cell and molecular biology · 2025Article
- Protein phosphatase PP2C19 controls hypocotyl phototropism through the phosphorylation modification of NONPHOTOTROPIC HYPOCOTYL3 in Arabidopsis.Plant & cell physiology · 2025Article
- Investigating the mechanism of chloroplast singlet oxygen signaling in thePlant signaling & behavior · 2024Article
- CAX-INTERACTING PROTEIN4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.Plant physiology · 2024Article
- CO-EXPRESSED WITH PSI ASSEMBLY1 (CEPA1) is a photosystem I assembly factor in Arabidopsis.The Plant cell · 2024Article
- Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues.Nature communications · 2024Article
- An efficient sulfadiazine selection scheme for stable transformation in the model liverwort Marchantia polymorpha.Journal of experimental botany · 2024Article
- CXIP4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.bioRxiv : the preprint server for biology · 2024Article
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5 authors.
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Abstract
T-DNA insertion mutants are very valuable for reverse genetics in Arabidopsis thaliana. Several projects have generated large sequence-indexed collections of T-DNA insertion lines, of which GABI-Kat is the second largest resource worldwide. User access to the collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch (http://www.GABI-Kat.de). Several significant improvements have been implemented recently. The database now relies on the TAIRv10 genome sequence and annotation dataset. All FSTs have been newly mapped using an optimized procedure that leads to improved accuracy of insertion site predictions. A fraction of the collection with weak FST yield was re-analysed by generating new FSTs. Along with newly found predictions for older sequences about 20,000 new FSTs were included in the database. Information about groups of FSTs pointing to the same insertion site that is found in several lines but is real only in a single line are included, and many problematic FST-to-line links have been corrected using new wet-lab data. SimpleSearch currently contains data from ~71,000 lines with predicted insertions covering 62.5% of the 27,206 nuclear protein coding genes, and offers insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre.
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