Hi Chunjiang, The TS miRNA sites track on hg18 was built in 2007 from version 4.0 of TargetScan, which did predict the hsa-miR-324-3p target site on MST1R. I visited the TargetScan website, and it is currently on version 5.1, which doesn't seem to predict the miR-324-3p target site on MST1R. I would suggest exploring the TargetScan release information page (http://www.targetscan.org/vert_50/docs/help.html) to figure out what changed from release 4.0 to release 5.1. If you still have questions, you could contact wibr-bioinformatics at wi dot mit dot edu.
To see the TargetScan version 4 MSTIR page naming the miR-324-3p predicted target site, in hg18 on the UCSC browser, turn on the UCSC Genes and TS miRNA sites tracks, and then enter "MST1R" in the search box labeled "gene" above the browser image. In TS miRNA sites track, click on the item labeled MST1R:miR-324-3p to see the details about this record. Click on the TargetScan link and it will take you to the TargetScan version 4 record. Please note, that on the more recent human assembly, hg19, we have a TS miRNA sites track that we released in December of 2010 and was built from TargetScanHuman 5.1. For more information about this track, please see the track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=targetScanS). Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group chunjiang he wrote, On 02/17/11 17:14: > Dear Mr/Ms, > Recently my colleague ask a question. > When he search targetscan target sites on genome browser (hg18), he found > microRNA hsa-miR-324-3p has a target sites on MST1R. > But when he check on TargetScan.org, he dont find it, even in ftp files. > After I check on PITA database, I found PITA has predicted a non-conserved > target sites for hsa-miR-324-3p on MST1R. > But I also dont find in TargetScan website. > So if there any different between collection of targetscan prediction in > UCSC and targetscan website. > Thanks, > Best, > Chunjiang > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
