GENCODE: producing a reference annotation for ENCODE
Open accessAbstract
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 annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. Results: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. Conclusion: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.
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Recurrent rearrangements implicated in genomic disorders are hypothesized to be associated with local genome architecture, such as segmental duplications that facilitate non-allelic homologous recombination.
“Recurrent rearrangements, implicated in genomic disorders, are hypothesized to be associated with local genome architecture44, e.g., with segmental duplications that facilitate NAHR.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [44]
The analysis revealed a map of structural-variant hotspots that may constitute local centers of de novo structural-variant formation, consistent with local genome architecture contributing to genomic instability.
“our analysis revealed a map of SV hotspots that may constitute local centers of de novo SV formation, consistent with the concept that local genome architecture contributes to genomic instability44.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [44]
A large percentage of common differentially expressed transcripts (48%, or 5,500 probes) are poorly annotated, including probes not mapped to the human genome, mapped to contig sequences, or not mapped to known GENCODE genes.
“a large percentage of these common differentially expressed transcripts (48%, or 5,500 probes) are poorly annotated, including probes not mapped to the human genome (HG19; http://genome.ucsc.edu/cgi-bin/hgGateway), mapped to contig sequences, or not mapped to known GENCODE genes21.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [21]
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- Authors
- Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., Rossier, C., Ucla, C., Hubbard, T., Antonarakis, S. E., & Guigo, R.
- Affiliations
- Wellcome Sanger Institute (GB)
- University of Geneva (CH)
- University of Lausanne (CH)
- Universitat Pompeu Fabra (ES)
- Corresponding author
- Harrow, Jennifer
- ORCID
- Venue
- Genome Biology
- Published
- 2006-08-07
- Volume
- 7
- Issue
- S1
- Pages
- S4.1-9
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC1810553
- OpenAlex
- W2169674658
- Cited by
- 648
- References
- 38
- Citations by year
- 2026: 11 · 2025: 18 · 2024: 23 · 2023: 23 · 2022: 26 · 2021: 43 · 2020: 27 · 2019: 27 · 2018: 33 · 2017: 31 · 2016: 36 · 2015: 37 · 2014: 34 · 2013: 49 · 2012: 71
- FWCI
- 11.41
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- IRIS (submittedVersion)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (submittedVersion, other-oa)
- Hispana (submittedVersion, other-oa)
- Research Portal (King's College London) (submittedVersion, other-oa)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- SERVAL (Université de Lausanne) (submittedVersion, other-oa)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- European Commission
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Human Genome Research Institute (U24HG007234)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- GENCODE, ENCODE, human genome annotation, protein-coding genes, novel exons, alternative splicing, splice variants, 5' RACE, RT-PCR validation, novel transcripts
- MeSH terms
- Chromosome Mapping, Genes, Humans, Proteins, Pseudogenes, Reference Standards, RNA, Messenger, Genome, Human, Sequence Analysis, DNA, Sequence Analysis, RNA, Computational Biology, Expressed Sequence Tags, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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