Hello Carla, The blocks in the mRNA/Genomic Alignments are in the same order as they appear on the genome. The structure is such that a block would not correspond to an intron, in the way that you are asking. To prove this to yourself, you can select one of the blocks you see in the mRNA/Genomic Alignments page, and BLAT this against the assembly you are viewing.
For example, If I want to look at the gene "ACTA1", I click on the refSeq Genes item, I click on mRNA/Genomic Alignments, and I click on "Block 1". I highlight the sequence for Block 1 (pasted here): CCACCGCAGC GGACAGCGCC AAGTGAAGCC TCGCTTCCCC TCCGCGGCGA 227636417 CCAGGGCCCG AGCCGAGAGT AGCAGTTGTA GCTACCCGCC CAG And then paste that into BLAT: http://genome.ucsc.edu/cgi-bin/hgBlat >From there it can be seen that this first block aligns on the 5' end of the >ACTA1 gene. Is that the topic you were struggling with? If you were looking for how to retrieve introns, let us know a little more about what you are trying to do, and hopefully we can assist you further. Also, please see the details page for refGene as it lists information about how the alignments were done and talks about the display conventions we use: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr1&g=refGene Open Helix also has some guides for getting started on the Genome Browser: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml I hope this information is helpful to you. Please don't hesitate to contact us again if you require futher assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- [email protected] wrote: > -- Hi! > I don't know if you would be the right person to ask, but I will do it > anyway... > I'm just starting to use de UCSC Genome Browser and have a basic > doubt: > when I click on the RefSeq Gene, then in the mRNA/Genomic Alignments > how do I know wich block correspond to which of the gene introns??? > I hope you can help me... > Thank you in advance. > Carla > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
