This track is part of the Repeats collection of the zebra finch telomere-to-telomere hub.
Transposable elements are sequences that copy or move themselves around the genome, and over evolutionary time they accumulate as fossilized copies that make up a large share of the DNA. Bird genomes are dominated by one family in particular, the CR1 LINEs, and are unusually poor in transposable elements compared with mammals. This track shows about 530,000 annotated elements and interspersed repeats.
Each element is drawn in the color that the source annotation assigns to its repeat family, so related families share a hue but the mapping is not a small fixed set of categories. The family name and its classification are on the details page of each item, together with the sequence ontology term and the identity to the library consensus. The track is set to dense by default because of the number of elements.
Repeats were annotated with a combination of de novo and curated resources. EDTA2 and RepeatModeler were used for de novo identification and their output was processed through RepeatMasker. EDTA was run with several curated libraries: zebra finch specific high-frequency repeats, a library built from bTaeGut1.4, RepBase, and a set of CR1 elements. The resulting repeat library was then curated with TEtrimmer v1.5.4 and the consensus sequences were checked by hand, with classifications corrected where coverage, self-alignment and conserved domain evidence disagreed with the automatic call. The curated library was fed back to EDTA with the --curatedlib option to reannotate the genome.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/repeats/bTaeGut7v0.4_MT_rDNA.EDTA2.v0.2.gtf.gz. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The GTF file uses GFF3-style attributes, so it does not parse as a gene annotation; each line was therefore converted to one BED feature, keeping the feature type and the full attribute string as extra fields and the color attribute as itemRgb. 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=transposons.
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/transposons.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
Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019 Dec 16;20(1):275. PMID: 31843001; PMC: PMC6913007
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.