This track is part of the Genes and Retrocopies collection of the zebra finch telomere-to-telomere hub.
A retrocopy arises when a messenger RNA is reverse transcribed and inserted back into the genome. Because the copy is made from spliced RNA it has no introns, and it usually lands far from the gene it came from. Most retrocopies decay into pseudogenes, but some acquire regulatory sequence and become expressed genes in their own right. This track shows 151 retrocopies that survived filtering and had expression support.
Retrocopies are drawn as gene models named after the parent gene they derive from. Clicking an item opens a page with its structure.
Retrocopies were identified with an improved version of the RCPedia pipeline. Messenger RNA sequences of annotated protein-coding genes were extracted with gffread and aligned to the genome with LAST (lastal -D1000). A candidate was kept if the alignment exceeded 120 bp, lay at least 200 kb from the parental locus, and preserved at least one of the last three exon-exon junctions of the parent transcript. Alignments with 40 percent or more repetitive sequence were discarded, as were candidates overlapping three or more annotated exons or coming from gene families with more than five redundant copies. Expression was then filtered against a simulated background: paired-end RNA-seq excluding exonic retrocopy regions was simulated with SANDY v1.0 and quantified with kallisto v0.48.0, and any retrocopy detectable in the simulation was dropped as unreliable. Remaining retrocopies were quantified on seven real RNA-seq datasets and kept only when supported by at least one uniquely mapped read from STAR v2.7.7a.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/retrogenes/bTaeGut7v0.4_MT_rDNA.RCPedia.v0.1.gff. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The GFF was converted to a genePred with gff3ToGenePred and then to bigGenePred. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=retrocopies.
For automated download and analysis, this annotation is a bigBed file inside the hub. Individual regions or the whole annotation can be obtained with bigBedToBed, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigBedToBed <hubUrl>/GCF_048771995.1/retrocopies.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
The original annotation 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
Conceição HB, Mercuri RLV, de Castro MPM, Ohara DT, Guardia GDA, Galante PAF. RCPedia: a global resource for studying and exploring retrocopies in diverse species. Bioinformatics. 2024 Sep 2;40(9). PMID: 39240653; PMC: PMC11387616
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.