Hi everyone, I just realized that annotations in the Biomart Database have not been updated to reflect changes at ENSEMBL. The Dataset is labeled as NCBIM37 (mm9), but the resulting output is actually NCBIM38 (mm10 dataset)
Steps to reproduce the isse: I choose the Gene "Il2" as the coordinates here have changed. Navigate to http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&datasets=mmusculus_gene_ensembl Filters: Filters->Gene->ID list limit-> MGI symbol enter "Il2" (IL2) Output: Atributes->Features->Gene->ENSEMBL-> Activate: Gene Start (bp) Gene End (bp) Result: GeneStart: 37120523 GeneEnd: 37125959 http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&datasets=mmusculus_gene_ensembl&step=4&id_list_limit_filters%5B%5D=mgi_symbol&id_list_limit_filters%5B%5D=Il2&id_list_limit_filters%5B%5D=MGI+symbol+%5Be.g.+Gm687%5D&attributes=transcript_start%2Ctranscript_end%2Cend_position%2Cstart_position%2Cchromosome_name%2Cexternal_gene_id Those results are from the mm10 dataset (verify here: http://useast.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000027720;r=3:37120523-37125959;t=ENSMUST00000029275 Expected for the mm9 dataset would be: GeneStart: 37019445 GeneEnd: 37024881 http://may2012.archive.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000027720;r=3:37019445-37024881 Is it possible to select the output to reflect a specific assembly? Thanks for your help, Jonas -- ______________________ Jonas Marcello Tarakhovsky lab The Rockefeller University 1230 York Ave New York, NY 10065 +1-212-327-8265
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