Hello, I thank the following people who responded my question posted several days ago. Now I received a couple of great responses. Please see the following messages. (1) From Jason E Stajich this is documented at the ensembl site, I would read more on their help pages and just looking at the base folder ftp://ftp.ensembl.org/pub For your question you want the GTF file: ftp://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh37.69.gtf.gz (2) From Micha³ Kabza Ensembl FTP (http://www.ensembl.org/info/data/ftp/index.html) contains GTF files with exon positions or you can download them using BioMart (http://www.ensembl.org/biomart/martview) . There is no explicit intron representation of introns in Ensembl, however. I've recently developed software that can help with your problem. It's available at http://galago.amu.edu.pl/wendigo/. You can use the SQLite databases from the webpage or use Python modules to access them. Keep in mind that Wendigo uses 0-based coordinates (exactly like UCSC, unlike Ensembl). Currently it has no citation, but the paper is under review in BMC Genomics. (3) From Anna You can get the exon and intron positions from UC Santa Cruz genome browser (http://genome.ucsc.edu/). Below are links to answers to questions similar to yours. https://lists.soe.ucsc.edu/pipermail/genome/2011-August/026943.html http://seqanswers.com/forums/showthread.php?t=3D5803 (4) From Mehmet Somel I get the positions from Ensembl Biomart: http://www.ensembl.org/biomart/martview/ In attributes, you choose "structures". (5) From Timothy O'Connor It depends on which gene models/annotation you decide to use. One tool that should give you what you want, plus a whole lot more, is SeattleSeq (http://snp.gs.washington.edu/SeattleSeqAnnotation137/). At the end of the list of things to include is two different gene model annotations where you can choose one or both versions. For large lists of variants it might be best to use the custom format split into multiple files. But it also has the capacity to directly annotate VCF files (which also may need to be split if the number of variants is greater than 500K). (6) From Julien Roux You can find this in the GTF file describing the gene models. It can be downloaded together with the genome sequence file from: http://useast.ensembl.org/**info/data/ftp/index.html ----- Hello, I am working on the human genome version GRCh37 in Ensembl (ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens). The files have gene position information, but do not have exon and intron position. Is there anyone who can tell where I can find it? Best regards, Haiwei Luo Visiting post-doc in Indiana University Haiwei Luo hluo2006@gmail.com