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GENCODE

Definition
AI-generated

GENCODE is a reference gene annotation project for human and mouse that aims to catalog protein-coding genes, splice isoforms, and noncoding transcripts on the reference genome, combining automated pipelines with manual curation.

Topics
Post-GWAS
URL
https://www.gencodegenes.org/
Related
Canonical Transcript Ensembl Genome Annotation

Why it matters in GWAS

VEP and many pipelines default to GENCODE (or Ensembl transcripts derived from the same effort); eQTL and TWAS studies typically report effects relative to specific GENCODE versions. Reproducible cross-cohort analysis requires noting the GENCODE (or Ensembl) release and transcript set.

Example usage

"We annotated variants with Ensembl VEP using GENCODE Comprehensive on GRCh38."

Canonical Transcript Ensembl Genome Annotation Genome-Wide Association Study (GWAS) MANE RefSeq Variant Annotation
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Mudge JM, et al. (2025). GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Res.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
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