Hello Riddhiman Dhar, It seems that you are viewing the Saccharomyces Genome Database track (the SGD track) in the Assembly browser and comparing that track's coordinate data to the ensGene.txt table (Ensembl track) from the downloads area.
The Ensembl and the Saccharomyces Genome Database tracks are generated independently and if the data differ, that is not a database problem, it is a problem with the annotation created by the source. The data within each track is consistent with itself. You will need to decide which annotation source to use/trust. You may need to do this on a gene-by-gene basis. There are no plans to update annotation at this time. However, you are welcome to upload as a custom track any published or curated annotation for the yeast genome that you create/find. http://genome.ucsc.edu/FAQ/FAQcustom I agree that this particular ensGene YNL177C is wrongly called (from a scientific perspective). But the data is consistent through all four data sources 1) mySQL 2)Downloads 3)Assembly Browser 4)Table Browser). The translation is based on the -3 frame, which is full of start and stop codons. The -2 frame looks much better, with a Met at positions A(304612),T(304611),G(304610) and a stop codon at positions T(303685),G(303684),A(303683). The SGD Genes track appears to get it right, picking the correct frame/coordinates. Jennifer Jackson UCSC Genome Bioinformatics Group Riddhiman Dhar wrote: > Hi, > Even if I consider for +1 base shift for the start position sometimes > the end position is not matching. Moreover, there are genes which are > 4-5 base shifted between the genome browser and the ensGene.txt (e.g., > YNL177C) > > Thanks, > Riddhiman 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
