Frankish, AdamAdamFrankishDiekhans, MarkMarkDiekhansJungreis, IrwinIrwinJungreisLagarde, JulienJulienLagardeLoveland, Jane EJane ELovelandMudge, Jonathan MJonathan MMudgeSisu, CristinaCristinaSisuWright, James CJames CWrightArmstrong, JoelJoelArmstrongBarnes, IfIfBarnesBerry, AndrewAndrewBerryBignell, AlexandraAlexandraBignellBoix, CarlesCarlesBoixCarbonell Sala, SilviaSilviaCarbonell SalaCunningham, FionaFionaCunninghamDi Domenico, TomásTomásDi DomenicoDonaldson, SarahSarahDonaldsonFiddes, Ian TIan TFiddesGarcía Girón, CarlosCarlosGarcía GirónGonzalez, Jose ManuelJose ManuelGonzalezGrego, TiagoTiagoGregoHardy, MatthewMatthewHardyHourlier, ThibautThibautHourlierHowe, Kevin LKevin LHoweHunt, TobyTobyHuntIzuogu, Osagie GOsagie GIzuoguJohnson, Rory BaldwinRory BaldwinJohnsonMartin, Fergal JFergal JMartinMartínez, LauraLauraMartínezMohanan, ShamikaShamikaMohananMuir, PaulPaulMuirNavarro, Fabio C PFabio C PNavarroParker, AnneAnneParkerPei, BaikangBaikangPeiPozo, FernandoFernandoPozoRiera, Ferriol CalvetFerriol CalvetRieraRuffier, MagaliMagaliRuffierSchmitt, Bianca MBianca MSchmittStapleton, EloiseEloiseStapletonSuner, Marie-MartheMarie-MartheSunerSycheva, IrinaIrinaSychevaUszczynska-Ratajczak, BarbaraBarbaraUszczynska-RatajczakWolf, Maxim YMaxim YWolfXu, JinuriJinuriXuYang, Yucheng TYucheng TYangYates, AndrewAndrewYatesZerbino, DanielDanielZerbinoZhang, YanYanZhangChoudhary, Jyoti SJyoti SChoudharyGerstein, MarkMarkGersteinGuigó, RodericRodericGuigóHubbard, Tim J PTim J PHubbardKellis, ManolisManolisKellisPaten, BenedictBenedictPatenTress, Michael LMichael LTressFlicek, PaulPaulFlicek2024-09-212024-09-212021-01-08https://boris-portal.unibe.ch/handle/20.500.12422/45346The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.en600 - Technology::610 - Medicine & healtharticle10.48350/1510513327011110.1093/nar/gkaa1087