This track is part of the Genes and Retrocopies collection of the zebra finch telomere-to-telomere hub.
This track shows protein-coding and long non-coding RNA gene models built by NCBI's eukaryotic genome annotation pipeline. Models are constructed from alignments of RNA sequencing reads and of proteins from related species, combined with ab initio prediction, so each transcript reflects both direct expression evidence and similarity to known genes. The track contains about 142,000 transcripts.
Transcripts are drawn in the standard gene model style: boxes for exons, thin lines with arrowheads for introns showing the direction of transcription, and thicker boxes for the coding part of each exon. Clicking a transcript opens a page with its identifier and structure.
Both haplotypes were annotated with the public version of NCBI's Eukaryotic Genome Annotation Pipeline, EGAPx v0.4.1 (github.com/ncbi/egapx), which combines RNA-seq and protein alignments with ab initio modelling. A set of 33 Illumina RNA-seq datasets covering a range of tissues and developmental stages was used, drawn in part from NCBI BioProjects PRJNA1032078, PRJNA516733 and PRJNA977995. Curated RefSeq and RNA-seq supported model RefSeq proteins from human, chicken, song sparrow, barn swallow and other sauropsids provided additional support, and one-to-one orthologs of human protein-coding genes were computed from protein homology and local synteny.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/genes/bTaeGut7v0.4_MT_rDNA.EGAPx.v0.1.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 was converted to a genePred with gtfToGenePred and then to bigGenePred, so exon structure and coding boundaries are preserved. 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=egapx.
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/egapx.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
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.