Blast
Enter sequence(s) below. FASTA format accepted.
Database:

The “Genome”, “Gene Model” and “Transcript” sequences are based on the JGI P. trichocarpa v3.0 release. The “Promoter” sequences extend 2-kb upstream of the start codon. Note that the exact promoter sequence for each gene needs to be empirically determined, and some intergenic regions are less than 2-kb. The 2-kb version is provided for maximum flexibility (e.g., the sequences can be trimmed for specific genes of interest).

Follow the “Get sequences” link on the output page to retrieve gene model, transcript and/or promoter sequences from the selected genome. For the sPta717_v1.1 genome, a “degenerate” version of the sequences incorporating SNPs/indels is also provided.

In degenerate sequences, SNPs are shown in IUPAC nucleotide code. Indels are shown in braces with the format: {reference allele, alternate allele}. Dashes signify gaps.

Example of a deletion in the alternate allele:
Reference allele:    ACAAGWAAAGAAAAGAAACAAGYGGTG
Alternate allele:    ACAAGWAAAGAAA-----CAAGYGGTG
Degenerate version:  ACAAGWAAAGAAA{A,-}{G,-}{A,-}{A,-}{A,-}CAAGYGGTG

Example of an insertion in the alternate allele:
Reference allele:    TGGTCAGGTATG----CATGCCYCCTTCATT
Alternate allele:    TGGTCAGGTATGTATGCATGCCYCCTTCATT
Degenerate version:  TGGTCAGGTATG{C,TATGC}ATGCCYCCTTCATT