Hello, Using your example YMR280C, in the yeast database S. cerevisiae Oct. 2003 Assembly, I found the gene "S. cerevisiae Gene CAT8" in the SGD Genes track at position chr13:827,028-831,329. The alignment is in the -3 frame and starts with an ATG (M). From drilling down into the alignment, I did not find any stop codons.
To view the data I did the following: 1. Did a position/search on YMR280C 2. Turned off all other tracks besides Base Position and SGD Genes 3. Set both of those tracks to full and set SGD Genes track controls as "Color track by codons:" to "genomic codons". (Click on the track name to see the description page and any track-specific display controls and the "Date last updated") 4. Clicked on the ---> arrow on the very left of the Base Position track in the display window to make it <--- 5. Zoomed/moved along the alignment length to view details at base level. Try viewing the data using these methods and let us know if you have additional questions, Jennifer Jackson UCSC Genome Bioinformatics Group Riddhiman Dhar wrote: > Hi, > I am using the yeast genomic sequence data and annotation data (ensGene.txt) > from UCSC genome Browser. However, the positions(i.e, start and end > position) of few Genes (e.g., YMR280C in the -ve strand from chr13 831328 to > 827027) do not match the nucleotide sequence of the gene from SGD and also > do not start with ATG. I noticed this when I was trying to read the codons > of the genes and sometimes "stop" codon appear in the middle of the gene. > Please tell me if there is any updated version of the gene annotation for > yeast. > > Thanking you > Sincerely, > Riddhiman Dhar > Department of Biochemistry > University of Zurich > Switzerland > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
