While around 62% of GENCODE coding loci have support for identification of the TTS of the locus, the picture is less clear at the TSS. Around 65% of GENCODE annotated TSSs do not overlap with CAGE tag clusters generated by the ENCODE transcript subgroup (Djebali et al. 2012). One likely reason for the disparity between the validation of the two ends of the gene is the limited tissue coverage of the TSS set, which is derived from 24 whole-cell line polyA+ CAGE experiments (Djebali et al. 2012).
