Most DNA in a cell is the familiar right-handed B-form double helix, but particular sequences can fold into other shapes: four-stranded G-quadruplexes, left-handed Z-DNA, hairpins formed by inverted repeats, and three-stranded triplexes. These structures can stall replication and transcription, they are associated with elevated mutation rates, and they are enriched in exactly the regions that were hardest to assemble. This track shows 11.3 million predicted motifs in eight classes.
Each motif is drawn in the color of its class. The class, the motif length and the sequence signature are in the item name and on the details page.
| G4, G-quadruplex predicted by Quadron | |
| Z, Z-DNA forming motif | |
| APR, A-phased repeat | |
| DR, direct repeat | |
| IR, inverted repeat, able to form a cruciform | |
| MR, mirror repeat | |
| TRI, triplex-forming motif, extracted from the mirror repeats | |
| STR, short tandem repeat |
Because there are more than eleven million motifs, the track is set to dense by default and stops drawing above the window size inherited from the original session. Zoom in to see individual motifs.
A-phased repeats, direct repeats, inverted repeats, mirror repeats, short tandem repeats and Z-DNA motifs were annotated with gfa. Triplex motifs were marked by gfa and extracted from the mirror repeat set. G-quadruplexes were predicted with Quadron; predictions with a score of NA were removed, which Quadron produces for sequence within 50 bp of the end of an input sequence, typically one or two motifs per chromosome.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/nonB/bTaeGut7v0.4_MT_rDNA.gfa%2BQuadron.sorted.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=nonBdna.
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/nonBdna.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
Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. Nucleic Acids Res. 2011 Jan;39(Database issue):D383-91. PMID: 21097885; PMC: PMC3013731
Sahakyan AB, Chambers VS, Marsico G, Santner T, Di Antonio M, Balasubramanian S. Machine learning model for sequence-driven DNA G-quadruplex formation. Sci Rep. 2017 Nov 6;7(1):14535. PMID: 29109402; PMC: PMC5673958
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.