Basic sequence data and description
All basic genomic and protein sequence data were downloaded from publicly available servers.
Plant genome project / database
|ARAMEMNON 8||ARAMEMNON 7|
TAIR Arabidopsis thaliana Database
MSU Rice Genome Annotation
RAP Rice Annotation Project
Grapevine Genome Project
Maize Genome Project
Poplar Genome Project
Brachypodium Genome Project
Tomato Genome Sequencing Project
Banana Genome Hub
Many gene loci have two or more cDNAs/proteins predicted (splice variants). They are included in the database with separate predictions for sequence and topology. For protein cluster calculations the longest predicted protein sequence of each gene locus is used. For each protein sequence the theoretical molecular weight and the isoelectric point (pK values according to Bjellqvist et al. 1994) are calculated.
Conserved protein domains (PFAM), Gene Ontology terms (GO) and external links
All protein sequences are checked against conserved protein domains in the Protein Families database (PFAM 33.1) using the HMMER software.
Gene ontology terms are added if terms according to the Gene Ontology Consortium have been assigned by Gramene (rice), TAIR (Arabidopsis thaliana) or PLAZA (Brachypodium distachyon, poplar, grape, maize).
For all proteins an external link to the corresponding major resource database (see above) is provided. In addition, there are links to NCBI, UniProt and (for rice) to RAP.
Data about coexpression/expression are available for most of the Arabidopsis thaliana and many of the Oryza sativa genes (see Resource > Other resources > Gene (co)expression for details of the expression resources).