Search Genes and Transcripts

Search Genes and Transcripts is a page where users can search for genes and transcripts from various datasets available in GDR. Users can search for genes from various datasets: predicted genes from whole genome assemblies,a single non-redundant list of Rosaceae genes with gene symbols (GDR Gene Database), or gene and mRNA sequences parsed out from NCBI nucleotide database. These genes and mRNAs parsed out from NCBI sequences are aligned to the reference whole genome sequences when possible. When expert-contributed information is available, these gene names are associated directly with the predicted genes from whole genome assembly. Users can also search from transcripts from RefTrans sets, reference transcriptome sets built from all publicly available transcripts, or EST unigene contigs. For more detail, refer to 'Description of Gene and Transcript Dataset' page.

Please Note: All the search categories below, except the file upload, can be combined.

1. Genus/Species

Use these drop-down menus to limit results to genes from a specific genus or species. Once a genus is chosen, species for the genus are dynamically populated in the species dropdown. Major genera are listed on top of the Genus list under 'Common Selections' and the rest are listed as 'All options' in alphabetical order.

2. Dataset

Use this drop-down menu to limt the results to sequences from a specific dataset. Go to 'Description of Sequence Dataset in GDR' for more details. Multiple options can be selected by holding down the "Ctrl" key.

3. Genome Location

Users can limit their results of predicted genes by their genome location. When a genome assembly is chosen in the drop-down menu next to 'Dataset', the corresponding chromosome or scaffold names are dynamically displayed in the 'Genome Location' drop-down menu. Choose any option and then type in the position in bp in the text boxes.

4. Gene/Transcript Name

Users can search genes and transcripts by name for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. The search is case-insensitive. Example gene names are MADS1, LFY2, or ppa027130m. Gene or transcript names in a file, separated by a new line, can be uploaded to do a batch search.

3. Keyword

Users can limit their result by associated funcitonal terms. Predicted genes from whole genome assembly and transcripts have been annotated with some of the followings: homology to genes of closely related or plant model species, InterPro protein domains, GO terms, KEGG pathway and ortholog terms. Users can enter any protein name (eg. polygalacturonase), KEGG term/EC number (eg. resistance, EC:, GO term (eg. cell cycle, ATP binding), or InterPro term (eg. zinc finger) in the text box to limit the results with the entries that are associated with the functional annotation terms.

If you have any questions/comments/feedback about this search page, please let us know via the contact form.