This track is part of the Repeats collection of the zebra finch telomere-to-telomere hub.
Satellite DNA is tandemly repeated sequence present in very long arrays, usually in centromeric and subtelomeric heterochromatin. Individual satellite families are often specific to one species or a small group of species, which makes them useful markers of chromosome structure and evolution. This track shows 901 satellite arrays assigned to named families.
Each array is drawn as a single feature named after its satellite family, for example Tgut716A, or TEL for terminal telomeric repeat.
Satellite sequences were identified de novo with SRF, run on the assembly, and with TAREAN, run on unassembled Nanopore reads from zebra finch testis after several rounds of subsetting with seqtk. Sequences of 20 bp or shorter were discarded and the rest were curated by hand. Further satellites were found by inspecting the repeats next to gaps in earlier zebra finch assemblies. RepeatMasker v4.1.5 was then used to place the resulting satellite set on the assembly. The satellite catalog was built with Satellome (github.com/aglabx/satellome).
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/repeats/bTaeGut7v0.4_MT_rDNA.satellome.v0.1.bed. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. 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=satellome.
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/satellome.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.