+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. +