The Ensembl project explicit aims to predict long intergenic non coding RNAs (lincRNAs) using a similar scheme (ie, histone modification patterns) and ESTs/cDNAs without coding potential in both Human and Mouse. They are explicitly characterised as lincRNAs. Like all our "predictions", they are biased towards a high specificity set and backed up by experimental evidence.
An example one is here: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000245883;r=7:99517494-99522910;t=ENST00000499990 Looking into the corresponding import of Ensembl into UCSC here: http://genome.ucsc.edu/cgi-bin/hgc?hgsid=173968291&o=99517493&t=99522910&g=ensGene&i=ENST00000499990 This transcript is there, but I can't spot the "biotype" slot here - it is just that it is non coding (we have about ~20 other non coding biotypes, eg, snoRNAs, miRNAs etc) (Is this true - UCSC guys, would it be possible to get the concept of BioType in the Ensembl set?) Also the Havana project, which does manual curation, which is both merged in a principled way with the Ensembl set (ie, the Ensembl set is a super-set of Havana at the point of release) and is available in UCSC browser also has a large set of non coding RNAs. A count of lincRNAs in Human and Mouse in Ensembl are: 1443 - in Human 407 - in Mouse. It is probably possible to either download from UCSC and the biotypes from Ensembl with a script to join or of course download the set from ensembl. You might like to use our BioMart tool: (showing our west coast mirror here) http://uswest.ensembl.org/biomart/martview/ On 2 Dec 2010, at 07:47, Bogdan Tanasa wrote: > Dear all, > > please could you recommend a track "Genes and Gene Prediction > Tracks" that > has the highest number (with good accuracy) of known/ predicted long > ncRNAs > (lincRNAs, etc) ? > > thanks, > > Bogdan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
