GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual/nannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results./nResults: The GENCODE gene features are divided into eight different categories of which only/nthe first two (known and novel coding sequence) are confidently predicted to be protein-coding/ngenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally/nverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been/nsequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,/n46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15/nputative transcripts. We assessed the comprehensiveness of the GENCODE annotation by/nattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out/nof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two/nof them in intergenic regions./nConclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of the/nGENCODE reference set available from the UCSC browser. Comparison of GENCODE/nannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within/nthe two sets, which is a reflection of the high number of alternative splice forms with unique/nexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE for/nEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human/ngenome with the aid of experimental validation.