Annotation Consensus Genome data sources Arabidopsis genome data is from TAIR (TAIR8). Rice genome data is from Rice Genome Annotation Project (Version 6.0). Populus genome data is collected from JGI (Version 1.1). Soybean genome data is compiled from phytozome (Version 1.0). Grape genome data is compiled from Genoscope (Version 1.0). Medicago genome data is from Medicago truncatula sequencing resources (Version 2.0). Maize genome data is from MaizeSequence.org (Update 20090301, the category of proteining coding sequences). Computational Prediction We use both computational prediction and manual curation to predict the members in each gene family. In computational prediction stage, we mainly use Interpro Scan supported by EBI. Foreach gene family prediction, the IPR ID used is as follow: E1: IPR000011   E2: IPR000608   SKP: IPR001232   RBX: IPR001841   cullin: IPR001373   ringfinger: IPR001841   HECT: IPR000569   BTB: IPR000210&IPR013069&IPR011333   Fbox: IPR001810   Ubox: IPR003613 Gene Locus A locus is a specific place on a chromosome where a gene is located, and could be taken equivalent as to a gene. In plantsUPS, more than one gene models could be derived from one locus. Gene Model A Gene Model is defined as any description of a gene product from a variety of sources including computational prediction, mRNA sequencing, or genetic characterization. Chromosome Number The chromosome number indicates the number of the gene's chromosome or linkage group. Gene Family We use automated prediction and manual curation in predicting which gene family the gene belongs to. Brief Gene Isoform The gene structure model image was created by bioperl module based on the information of exon and CDS in the gene. It is used to demonstrate the exons and CDS distribution along the gene. Interproscan Search InterProScan is a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation. Protein Sequence Features Image The images were generated based on Interproscan search results. It is used to demonstrate the protein domains distribution along the protein. RefSeq Database Blast We performed blastp against RefSeq protein database. Several top feedbacks were collected in plantsUPS in aim to study protein's features. Uniprot Database Blast We performed blastp against Uniprot (plant part) protein database. Several top feedbacks were collected in DPUPS in aim to study protein's features. GO Annotation The GO annotations were generated by protein Interproscan search. The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. Putative Ortholog To characterize the putative ortholog in other organisms, we performed Blast search. Proteins in other organisms which are best reciprocal (BR) marked "Y", otherwise "N". Distribution Map The chromosome map was created by GenomePixelizer. Each gene family was represented as one color-specific blocks. A color description image was provided, and can offer links to the family browse page. The genes on the up side of the chromosome line mean they on the plus chain, accordingly other side means minus chain. Multialignment The letters on the Consensus line have their specific meanings. The multialignments are performed by using functional domain of protein or full length sequences. The F-box family of poplar was applied multialignment using F-box domain which identified by InterproScan. Multialignment of each gene family is generated by clustalW and the displayed colorful alignment is modified by CHROMA (CHromatic Representation Of Multiple Alignments). Phylogenetic Tree The phylogenetic tree was constructed using ClutalX and the created by MEGA 4.0. They were constructed based on full-length sequences by using Neighbor-Joining method with 100 times bootstrap. Since the large number of members in F-box or ringfinger family, it is possible and reasonable the bootstrap score may be very low. There is no phylogenetic tree generated for gene families of some species whose members is less than 3. And we manually modified poplar Fbox and BTB families phylogenetic trees by display some obvious cluster colorfully aim to provide users better lookings.