sPta717 Variant DB - aspendb

sPta717 Variant DB (http://aspendb.uga.edu/s717)

Variant-substituted genome sequence of P. tremula x alba 717-1B4

The v2 included more SNPs/indels, a confidence rating assigned to the data presented and discrepancy between haplotypes. Note, the sPta717v1.1 searches are still available, and we have added P. deltoides WV94.

 

Funded by the Center for Bioenergy Innovation, a U.S. Department of Energy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science; the Joint Genome Institute, a DOE Office of Science User Facility; the National Science Foundation Plant Genome Research Program (IOS-1546867); and the Hank Haynes Georgia Research Alliance Forest Biotechnology Endowment.

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 & Genomes 11: 82.
Bewg WP, Ci D, Tsai C-J (2018) Frontiers in Plant Science 9: 1732

 

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

sPta717alba.fasta.gz 

sPta717alba_v2_gene.gff3.gz

sPta717alba_v2_gene_model.fa.gz

sPta717alba_v2_promoter.fa.gz

sPta717alba_v2_transcript.fa.gz

sPta717tremula.fasta.gz

sPta717tremula_v2_gene.gff3.gz

sPta717tremula_v2_gene_model.fa.gz

sPta717tremula_v2_promoter.fa.gz

sPta717tremula_v2_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_v2.0.vcf.gz (Allelic variants of sPta717_v2.0)

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

PdeltoidesWV94_v2.0.vcf.gz (Allelic variants of PdeltoidesWV94 v2.0)

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

 

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