The ENCODE4 long-read RNA-seq collection annotates trancripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This method reveals how promoter selection, splice pattern, and 3’ processing are deployed across -human tissues. +mouse tissues.
-Transcripts in this track have a string representing each triplet (e.g. [2,1,3]). Thus, transcripts
-with the same exon junction chain will share the middle digit in the string.
-
+Transcript names include a triplet annotation that represents transcript start site, exon junction
+chain, and transcript end site. For example, if transcript A has the label [1,2,3] and transcript B
+is labeled [1,1,3], then those transcripts share start and end sites but have a different combination
+of exons.
GENCODE V29 and V40 were used as reference data; any transcript not present in either of these is
-colored blue.
-
+colored blue.
Mouseover on transcripts shows their ENCODE gene ID and the tissue or cell line where it’s most highly expressed, and its TPM in that sample.
+The data underlying this track is available in the file +encode4LongRna.bb. +Individual regions or the whole genome annotation can be obtained using our +tool bigBedToBed, which is available on our +download server. +For example, to extract only annotations in a given region, you could use the following command: +
+ ++bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://hgdownload.gi.ucsc.edu/gbdb/$db/encode4LongRna.bb stdout ++ +
Please refer to our mailing list archives for questions, or our -Data Access FAQ +Data Access FAQ for more information.
-Data were retrieved from https://zenodo.org/records/15116042. The transcript gtf -was converted to Bed format, and expression and CDS data added from the relevant files using a -custom script. +Data were retrieved from https://zenodo.org/records/15116042. +The mouse_ucsc_transcripts.gtf was converted to BED format, and expression and CDS data +added from the relevant files using a custom script.
Thanks to Fairlie Reese for providing data access and for helpful feedback.
Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y et al. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv. 2023 May 16;. PMID: 37292896; PMC: PMC10245583