Home Page

Users can check news or notifications of plantsUPS at the home page. Five fundamental functions are available at left frame of web page (see red frames in the picture above). The browse and document parts have more than one selection.

Browse Page

User can use generic browse page to browse every gene family of eahc species. Foreach query, only one species is supported. The gene family and chromosome can be used seperately or simultaneously to refine the query results, or be set no limitation at all. For more than one family or chromosome request for better defined request, please use search function.

The browse result page has two basic parts: request summary and loci list. In the upper part of the page is a brief description of query set by user, and Matched gene number is represented. It further provides four types of download: peptide sequence, transcript sequence, CDS sequence and loci list. User should be noted that sequences provided by plantsUPS are based on gene model name and it is possible that one gene locus have two or even more gene models, in other word, number of sequences downloaded is possible larger than matched gene number. In lower part of the page, search results are exhibited by four columns. Click any gene name will link user to the gene's corresponding detailed information.

Users can find extensive information concerning the gene. There are seven parts in this page: Basic Information, Gene Structure, Protein Sequence Feature Details, GO Annotation, putative ortholog, micorarray data, blast search. Most of they are easy to understand and we provided detailed annotation in the annotation page. Abundant links are provided. The protein and transcript sequences of the gene are free to download, and so is the microarray probe sequence (if have). Two model images of each gene were produced, seperatedly demonstrating the gene's structure and the protein's structure. For genes have more than one gene model, user can swith gene model in the basic information table. In putative ortholog part, BR means best reciprocal and 'Y' means positive, while 'N' negative.

Select one species to view the corresponding distribution map. Because the maize genome is yet not finished completely, we currently provide no distribution map for maize. 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. Detailed gene family or gene information are accessible by click the blocks.

To browse multisequence alignment results, user should select one of seven species and define a gene family.

To browse multisequence alignment results, user should select one of seven species and define a gene family. Note: There is no phylogenetic tree generated for gene families of some species whose members is less than 3.

Search Page

Users should select at least one plant species in the following form, while selection of more than one organisms is supported. Gene family should be defined, or use "No Limited" to conclude all gene families. Further search request can be set by choosing certain query type and input corresponding content. If no results can be found based on advance search query, it will be treated as "Not valid" that actually give up this query restriction. The chromosome number is the number of the chromosome, for example: Chr1 is 1, or LG_II is 2.

Similar to the structure of browse result page, the search result page has two parts: a brief summary and request results. Request species and corresponding matched number are presented. Two types (peptide and loci list) download are available. The background color of gene name in results are prefined in tend to give user a clearer view.