sPta717 Genome

sPta717 Genome

Substituted genome sequence of P. Tremula x alba 717-1B4, created by

introducing genomic variants into the P. trichocarpa reference genome.

 

 

The new sPta717 search tools include more SNPs/indels, a confidence rating assigned to the data presented, discrepancy between haplotypes, and the ability to blast search either tremula or alba. Note that all of the sPta717v1.1 searches are still available.

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:

sPta717alba.fasta.gz 

sPta717alba_v2_gene.gff3.gz

sPta717alba_v2.0_gene_model.fa.gz

sPta717alba_v2.0_promoter.fa.gz

sPta717alba_v2.0_transcript.fa.gz

sPta717tremula.fasta.gz

sPta717tremula_v2_gene.gff3.gz

sPta717tremula_v2.0_gene_model.fa.gz

sPta717tremula_v2.0_promoter.fa.gz

sPta717tremula_v2.0_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_v1.1)

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

 P B GM

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