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Table 1 Definition of Geneset provenance

From: Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Geneset

Provenance

GENCODE Comprehensive

All transcripts at protein-coding genes. Includes transcripts with NMD, retained_intron and processed_transcript biotypes.

GENCODE Basic

Only full-length, protein-coding transcripts at protein-coding genes.

RefSeq NXR

All RefSeq transcripts at protein-coding genes. Includes manually annotated NM, NR and automated XM transcripts.

RefSeq NR

Only manually-annotated transcripts at protein-coding genes. Includes NM and NR transcripts

  1. Transcript functional biotypes and source e.g. manual or automated annotation, for the four genesets used in this study.
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BMC Genomics

ISSN: 1471-2164

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