Hi Tapas, The miRNA/sno track on hg18 shows miRNA (among other types of RNA). However, it does not contain information about whether an miRNA is intragenic or intergenic. To obtain a list of intergenic miRNA, you'll need to create several custom tracks using table browser tool. Below, I have provided instructions to guide you through the process.
1) Create a custom track of miRNA that don't overlap any Exons of UCSC Genes: Cick on "Tables" on the blue bar on the top of the main page and make the following selections: clade: Mammal genome: human assembly: Mar. 2006 (NCBI36/hg18) group: Genes and Gene Prediction tracks track: sno/miRNA table: wgRNA (you can click "describe table schema" to view descriptions of the table columns) region: genome filter: click on "create". Set "type" to "does" match and enter "miRNA" in the adjacent field. Click submit. intersection: click on "create". Set group to "Genes and Prediction tracks", track to "UCSC Genes", and table to "UCSC Genes (knownGene). Select "All UCSC Genes records that have no overlap with UCSC Genes" and click submit. output format: custom track Click "get output" and then enter a name and description for your custom track, I would suggest something like: name=non-Exonic miRNA description= miRNAs not overlapping with UCSC Genes Exons Click "get custom track in table browser" 2) Create UCSC Genes track of intronic regions: Make the following selections in the table browser: clade: Mammal genome: human assembly: Mar. 2006 (NCBI36/hg18) group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: genome output format: custom track Click "get output", enter a name and description like: name=Introns description=Introns from UCSC Genes and then select "Introns plus" (leaving "0" in the adjacent field for "bases at each end"). Click "get custom track in table browser" 3) Intersect non-exonic miRNA with Introns to get intergenic miRNA: clade: Mammal genome: human assembly: Mar. 2006 (NCBI36/hg18) group: Custom Tracks track: non-exonic miRNA (or whatever you named the custom track from step 1) table: default table (should only be one) region: genome intersection: click on "create". Set group to "Custom Tracks", set track to "Introns" and table to the default table (again, should only be one). Select "All non-exonic miRNA records that have no overlap with Introns" and click submit. output format: custom track Click "get custom track in genome browser", enter a name and description like: name=Intergenic miRNA description=Intergenic miRNA Click "get custom track in table browser" 4) Get the list of intergenic miRNA: clade: Mammal genome: human assembly: Mar. 2006 (NCBI36/hg18) group: Custom Tracks track: Intergenic miRNA (or whatever you named the custom track from step 3) table: default table (should only be one) region: genome intersection with ... : click "clear" if there is still an intersection showing, then it should just say "intersection:" output format: all fields from selected table Click "get output" You should now have a list of intergenic miRNA and their coordinates. For more information about using the Table Browser see "Using the Table Browser" by scrolling down past the Table Browser form. It provides brief descriptions of the Table Browser controls. You can also see the "User's Guide" at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group [email protected] wrote, On 08/27/10 06:04: > Respected Sir/Madam, > I am a senior research fellow at Indian Statistical > Institute Kolkata India. > > Currently I am involved in a bio-informatics related research. > For my research purpose I wanted to know the type of the > miccroRNA i.e whether it is intergenic or intragenic. How to > obtain the type of a given human miRNA? That is I want to list > out only all intergenice microRNAs. > > Thanking you, > Tapas Bhadra > Senior Research Fellow, > ISI Kolkata, > India. > > > This mail is scanned by Ironport > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
