Gene annotation places transcripts and their coding sequence on the assembly, using alignments of RNA sequencing reads and of proteins from related species. Alongside the ordinary gene models, this collection carries retrocopies: DNA copies of a messenger RNA that were written back into the genome by reverse transcription, which is why they lack the introns of the gene they came from.
This collection holds the EGAPx Genes and Retrocopies tracks. Each has its own description page with the details of how it was made, reachable from the track name in the browser or from the list below the configuration controls on this page.
The individual track description pages carry the download and intersection instructions for each annotation. The original files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.