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Related Experiment Videos

GENCODE: producing a reference annotation for ENCODE.

Jennifer Harrow1, France Denoeud, Adam Frankish

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK. jla1@sanger.ac.uk

Genome Biology
|August 24, 2006
PubMed
Summary
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The GENCODE project identified and mapped human protein-coding genes using manual annotation and experimental validation. This comprehensive gene set includes novel splice variants and improves genome annotation accuracy.

Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • The GENCODE consortium aimed to comprehensively identify and map all protein-coding genes within ENCODE regions.
  • Annotation involved manual curation by the HAVANA team and experimental validation.

Purpose of the Study:

  • To create a high-quality reference set of human protein-coding genes.
  • To experimentally validate and refine gene annotations.

Main Methods:

  • Manual gene annotation by the HAVANA team.
  • Experimental validation using 5' rapid amplification of cDNA ends (RACE) and RT-PCR.
  • Assessment of annotation comprehensiveness by testing predicted exon boundaries.

Main Results:

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  • Annotated 487 loci, with 434 confirmed as coding.
  • Experimentally verified over 50% of coding loci using 5' RACE.
  • Identified novel splice variants and validated new exon pairs.

    • Conclusions:

    • GENCODE provides a refined reference set of human genes, including extensive alternative splicing.
    • Experimental validation is crucial for accurate gene annotation.
    • Ongoing refinement of the human genome annotation is essential.