sPta717 Genome

Substituted genome sequence of P. Tremula x alba 717-1B4, created by introducing genomic variants into the P. trichocarpa reference genome.

 

Citations

Zhou X, Jacobs TB, Xue LJ, Harding SA, Tsai CJ (2015) New Phytologist 208: 298-301.
Xue LJ, Alabady MS, Mohebbi M, Tsai CJ (2015) Tree Genetics & Genomics 11: 82.

 

Download the sPta717 v2 (new version) sequence and annotation files:

sPta717_v1.1.fa.gz

sPta717_v2.gene.gff3.gz

sPta717_v2_gene_model.fa.gz

sPta717_v2_promoter.fa.gz

sPta717_v2_transcript.fa.gz

sPta717_v2_degenerate_gene_model.fa.gz

sPta717_v2_degenerate_promoter.fa.gz

sPta717_v2_degenerate_transcript.fa.gz

 

Download the sPta717 v1.1 sequence and annotation files:

sPta717_v1.1.fa.gz

sPta717_v1.1.gene.gff3.gz

sPta717_v1.1_gene_model.fa.gz

sPta717_v1.1_promoter.fa.gz

sPta717_v1.1_transcript.fa.gz

sPta717_v1.1_degenerate_gene_model.fa.gz

sPta717_v1.1_degenerate_promoter.fa.gz

sPta717_v1.1_degenerate_transcript.fa.gz

 

Download pre-designed, SNP-free gRNAs for 38,509 gene models:

sPta717gRNAs.csv

(from Zhou et al. 2015 New Phytologist DOI: 10.1111/nph.13470).

 

Download the Aspen CRISPR designer program:

AspenCRISPRdesigner.tar (Perl Scripts and help document)

 

Data Sets:

sPta717_v1.1.vcf.gz (Allelic variants of sPta717)

Ptrichocarpa_v3.0.vcf.gz (Variants between Populus trichocarpa and sPta717)

 

TESTING

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Probe Search 2 Test

Blast Search 2 Test

Gene Model 2 Search Test

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