This track is part of the Centromeres and Telomeres collection of the zebra finch telomere-to-telomere hub.
The centromere core is the part of the satellite array where the kinetochore actually assembles, and it is usually narrower than the full array and marked by a local dip in DNA methylation. This track shows 80 predicted centromere core regions, one or a few per chromosome arm.
Cores are drawn as single blocks. The details page carries the satellite motif the core was called on and the average methylation measured across it, which is the value that separates an active core from the surrounding array.
Centromeric cores were located bioinformatically from the satellite annotation and the methylation signal, and checked against the mapped centromere markers. The scripts used in the centromere analyses are at github.com/gf777/T2T-zebra-finch.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/centromeres/bTaeGut7v0.4_MT_rDNA.centromere_detector.v0.1.gff. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. Each GFF line became one BED feature, keeping the color attribute as itemRgb and the attributes, including the average methylation, as an extra field. 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=centroCores.
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/centroCores.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.