AtEnsembl now contains the TAIR7 Arabidopsis annotation, which was released in April 2007.
Greater than 1 million SNPs have been identified through sequence analysis of 20 different Arabidopsis ecotypes.
The latest data from sources including Uniprot, dbEST and EMBL has been aligned to the TAIR7 genome.
New release of CATMA database and annotation.
Click on a chromosome for a closer view
The data on this site is a direct import of the the TAIR Arabidopsis thaliana genome annotation database release 7. No additional genebuild was carried out, but a series of alignments were done to provide Affymetrix gene probes, UniProt hits, and other similarity data.
The MIPS genome annotation release 11_02_04 has been superimposed onto the TAIR sequence by converting MIPS genome coordinates into TAIR coordinates. This was achieved by mapping MIPS contigs to TAIR contigs using a variety of comparative tools. We estimate that 98% of MIPS genomic coordinates have been successfully converted into TAIR coordinates. For the approximately 2% of cases where this conversion was not possible an unconverted copy of the MIPS gene, displayed as 'shadow genes', has been approximately located on the TAIR genome by aligning it to the nearest known coordinate.
Coordinates for all inserts other than SALKs were provided by Sean Walsh at the John Innes Centre ( ATIDB ). SALK coordinates were obtained from the SIGNAL database at the SALK institute.
Brassica ESTs - Expressed Brassica sequences from public and proprietary sources are mapped using BLAST to identify candidate homologous genes on the Arabidopsis genome. Complete annotation for these expressed sequences may be can be viewed and searched using the linked Brassica ASTRA EST database at http://hornbill.cspp.latrobe.edu.au (Love et al.,2005).
Brassica rapa - As the first stage of the Multinational Brassica Genome Sequencing Project (www.Brassica.info), end sequences are being obtained for 110 000 B. rapa genomic DNA fragments maintained as Bacterial Artificial Chromosomes (BACs). These genomic sequences have been mapped onto candidate syntenic regions of the Arabidopsis genome based on paired end sequences sharing identity with Arabidopsis sequence within 500,000 bp and in complementary orientation to each other. Intervening BAC sequence may be assumed to share a high degree of synteny. Annotation for Brassica rapa BAC end sequences is provided through links to the B. rapa ASTRA database.
Brassica oleracea - In a collaboration between Cold Spring Harbor and TIGR 0.5 coverage whole genome shotgun sequences have been produced for B. oleracea. These sequences have been mapped onto the Arabidopsis genome by their most significant BLAST match. Complete annotation for these expressed sequences may be can be viewed and searched using the linked B. oleracea ASTRA database at http://hornbill.cspp.latrobe.edu.au
Love CG, Robinson AJ, Lim GA, Hopkins CJ, Batley J, Barker G, Spangenberg GC, Edwards D. (2005). Brassica ASTRA: A integrated database for Brassica genomic research. Nucleic Acids Research 33: D656-9.
| Assembly: | TAIR7 ( TIGR5, Jan 2004) |
| Genebuild: | TAIR7, April 2007 |
| Database version: | 41_1 |
| Gene predictions (incl. 3,889 pseudogenes): | 30,918 |
| Gene exons: | 167,212 |
| Gene transcripts: | 35,818 |
| Base Pairs: | 135,187,985 |
| Golden Path Length: | 119,186,497 |
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
