ArticleGenome research2012
GENCODE: the reference human genome annotation for The ENCODE Project.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,923 papers, 1 of them a synthesis that pooled it.
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Who cites it
2,923 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly.Nucleic acids research · 2026Article
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- Accurate de novo transcription unit annotation from run-on and sequencing data.PLoS computational biology · 2026Article
- The Impact of NEAT1 on Inflammatory Responses and Processes in Arthropathic Diseases: Latest Findings and Perspectives.Biochemical genetics · 2026Review
- Initial Genome-Wide Characterization of Turkmen Individuals from the Dashoguz Region, Turkmenistan.Biology · 2026Article
- Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.Nature communications · 2026Article
2,863 more citing papers are in PubMed but not listed here.
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Authors and funding
41 authors.
Funding
Abstract
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.