Gene Model Search
Enter gene model name to retrieve sPta717_v1.1 and Ptricho_v3.0 sequences.

Three types of sequences are provided based on the JGI P. trichocarpa v3.0 release: (1) gene model, including UTRs (when available), exons and introns (when available), (2) transcript, and (3) promoter.

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).

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