The genome data in PhytoMine are generated from organisms sequence by the JGI, collaborators and other members of the plant genome community. The genome annotations were done internally or by outside groups. Read more

Query for genomics:

• Gene & Proteins.
• Show the DNA sequence flanking a specified gene.
• Gene, Transcript, Protein names for a specific gene
• Show all CDSs for a specified gene with nucleotide sequence.
• Show all UTRs for a specified gene with nucleotide sequence.
• Show all mRNAs for a specified gene with nucleotide sequence.
• Gene Synonyms

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The annotated protein-coding transcripts from the Phytozome collection. Read more

Query for transcripts:

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The proteome for different organisms and their InterProScan analyses. Read more

Query for proteins:

• GO Terms for a transcript or list of transcripts
• GO Terms for a protein or list of proteins
• GO term lookup.
• GO-Annotations
• Peptide sequence for a specific transcript
• Children of a specific GO term

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Orthologs, paralogs and families of similar proteins. Read more

Query for comparative:

• All homologs of a specific gene in any organism
• Homologous genes in two specific species

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A compendium of RNA-seq data for organisms in Phytozome. Some data were acquired by members of the community. Recent data are unpublished data from the Plant Gene Atlas Project. Read more

Query for expression:

• Expression score for one specific gene
• Expression score for all genes in an organism
• Expression score for all mRNAs in an organism
• Expression of gene homologs in Arabidopsis

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