Dear Nicholas, The ensGene table has the Ensembl genes. If you would like to get the coordinates for particular Ensembl genes in hg19 you can use the table browser with the following settings:
genome: Human assembly: hg19 group: Genes and Gene Prediction tracks track: Ensembl Genes table: ensGene region: genome identifiers (names/accessions): click on paste list (paste the list of Ensembl Genes identifiers and click "submit") output file: selected fields from primary and related tables click "get output" Select the following: name Name of gene chrom Reference sequence chromosome or scaffold strand + or - for strand exonCount Number of exons exonStarts Exon start positions exonEnds Exon end positions click "get output" This will give you the coordinates for the Ensembl gene identifiers that you provide. Please note: all start coordinates in our database are 0-based, not 1-based. See explanation here: (http://genome.ucsc.edu/FAQ/FAQtracks#tracks1). Vanessa Kirkup Swing UCSC Genome Bioinfomatics Group ----- Original Message ----- From: "Nicholas Price" <[email protected]> To: [email protected] Sent: Thursday, February 3, 2011 8:30:37 AM Subject: Re: [Genome] Intron-removal Hi I am using the method below to fetch orthologous coding regions. When I define a region I use the coordinates from ensembl. In most cases the coordinates agree but in some cases they are different in UCSC. Is their a way to by pass this problem. Can I download the coordinates of the Ensembl genes as they are in UCSC.. Thank you Nicholas On 20 January 2011 17:23, Vanessa Kirkup Swing <[email protected]> wrote: > Dear Nicholas, > > Now that we know that you are looking for the orthologous protein coding > regions, there is a great tool in the table browser > (http://genome.ucsc.edu/cgi-bin/hgTables) to do this. > > Please set the following: > > genome: Human > assembly: hg19 > group: Genes and Gene Prediction tracks > track: Ensembl Genes > table: ensGene > region: click "define regions" and paste in your coordinates. > output file: CDS FASTA alignment from multiple alignment (this will get you > the orthologous protein coding regions) > > and click "get output". > > click the "+" button next to the primate to select all of the primates or > you can select the individual primates that you are interested in. > Note: There are formatting options at the top of this page that might be of > interest to you. > > click "get output". > > > Hope this helps! > > Vanessa Kirkup Swing > > > ----- Original Message ----- > From: "Nicholas Price" <[email protected]> > To: [email protected] > Sent: Thursday, January 20, 2011 9:14:39 AM > Subject: Re: [Genome] Intron-removal > > Hi > > I am trying to find orthologous protein coding regions in primates. I have > the coordinates of the Ensembl genes, however these coordinates include > introns and exons. SO when I use them the way you suggested below I will get > alignments that include exons and introns..SO I am trying to find a way to > get the only the protein coding part. For example a way that I could do it > is to get the coordinates of the exons that make the protein coding part of > the gene and then use multiz46 to get the orthologous regions....and in the > end concatenate them together.....However I am worried that the exon parts > are too small and may get ambiguous results. Is there another way which is > better??? I hope I am clearer this time.. > > Nicholas > > > > On 21 December 2010 16:54, Mary Goldman <[email protected]> wrote: > >> Hi Nicolas, >> >> I think I may not be fully understanding what you are asking. The way I >> read your question is that you have the coordinates of one human gene for >> which you are trying to find the primate ortholog using the Conservation >> track. You want only the coding region for this gene. If this is the case >> you can do the following using the Table Browser: >> >> genome: Human >> assembly: hg19 >> group: Comparative Genomics >> track: Conservation >> table: Multiz Align (multiz46way) >> region: click "define regions" and paste in your coordinates. >> intersection: click "create". Choose a gene prediction track and choose >> the radio button " All multiz46way records that have any overlap with >> 'gene prediction track'". Click "submit". >> output file: enter a name if you want to save the output as a file >> >> and click "get output". >> >> I'm sorry if I am not completely understanding your issue. Please send some >> clarifying information to the list if this does not resolve your issue (I >> may not be available due to the holidays - that is why it would be best if >> you could send it to the list). >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> ----- Original Message ----- >> From: "Nicholas Price" <[email protected]> >> To: "Mary Goldman" <[email protected]> >> Sent: Tuesday, December 21, 2010 1:10:29 PM >> Subject: Re: [Genome] Intron-removal >> >> Hi Mary >> >> >> I want to confirm that the answer you send me below is for getting >> orthologous pseudogenes and not on how to remove intronic regions >> >> >> Nicholas >> >> >> >> On 21 December 2010 13:45, Mary Goldman < [email protected] > wrote: >> >> >> Hi Nicolas, >> >> We recommend following the steps in this previous mailing list question: >> https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024414.html , >> except that when you create an intersection with your gene track of >> interest, choose "Base-pair-wise intersection" or "All Mulitz records that >> have any overlap ..." . >> >> I hope this information is helpful. Please feel free to contact the >> mail list again if you require further assistance. >> >> Best, >> Mary >> ------------------ >> Mary Goldman >> UCSC Bioinformatics Group >> >> >> >> >> ----- Original Message ----- >> From: "Nicholas Price" < [email protected] > >> To: [email protected] >> Sent: Tuesday, December 21, 2010 10:32:50 AM >> Subject: [Genome] Intron-removal >> >> Hi >> >> I want to find all the primate orthologs to a Human gene and retrieve only >> the coding region. I use the Human Genome, conservation track, comparative >> genomics, Multiz-Align. I put the coordinates of my gene..and I retrieve >> the >> alignments. I do all this from a perl script..I am wondering how to filter >> out the intronic regions ..etc and get only the coding region? Is there an >> option in Tables that does that? >> >> >> Nicholas >> -- >> The oppressed become the oppressors Paulo Freire (1921-1997) >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> -- >> The oppressed become the oppressors Paulo Freire (1921-1997) >> > > > > -- > The oppressed become the oppressors Paulo Freire (1921-1997) > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- The oppressed become the oppressors Paulo Freire (1921-1997) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
