Hello, The Conservation track contains genomic multiple alignments. Conserved elements are also noted. Gene bounds are not. Therefore, it would not be a possible choice as a starting base track to identify TSS (transcription start sites) in any of the genomes.
Instead, you can use a human gene prediction track or TSS track to location a genomic regions on the Conservation track that represent genes/TSS regions, then use these coordinates to identify coordinates on aligned genomes and locate native genes (meaning, use rat genomic coordinates to locate rat genes). Use the table browser to extract sequence based on genomic coordinates (many options to expand the region are offered, custom track BED file, etc.). Or, alter coordinates as needed using your own tools and extract from the genome fasta sequences directly. FTP help: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/FAQ/FAQdownloads#download27 Tools help: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities (faSomeRecords) Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group [email protected] wrote: > Dear Gbrowse team, > > regarding the multiple sequence alignments (43 way with human as reference) is > there an easy way to obtain the sequences ranging from the TSS to 1kb > DOWNstream > (instead of 1kb upstream)? > > Many thanks and best wishes! > > Helge > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
