+Regulatory elements often leave no mark in the genome sequence itself, but they do tend +to change more slowly over evolutionary time than the DNA around them. Comparing a +genome with those of related species therefore highlights the parts that are under +selection, and stretches outside genes that stay conserved are good candidates for +regulatory function. These are usually called conserved non-coding elements. +
+ ++This track holds conservation and CRISPR resources for danRer11 produced by the Shawn +Burgess laboratory at NHGRI, which the DANIO-CODE consortium includes in its track hub. +It has two parts. The conservation part is a phastCons score computed from an alignment +of zebrafish with grass carp, common carp and goldfish, together with the conserved +non-coding elements called from that score. The CRISPR part is a genome-wide catalogue +of predicted CRISPR/Cas9 target sites, in three sets: all target sites, those beginning +with GG, and those beginning with GA. The GG and GA sets matter in practice because +those dinucleotides are efficiently transcribed by the polymerases used to make the +guide RNA. +
+ ++This track is part of the DANIO-CODE collection. +
+ ++The phastCons track is a graph, auto-scaled to the window. The conserved non-coding +elements and the CRISPR target sites are drawn as blocks, in the colors stored in the +data files. All five tracks are off by default. +
+ ++The phastCons scores were computed from a whole-genome alignment of zebrafish with three +other cyprinid fishes, grass carp, common carp and goldfish, and conserved non-coding +elements were called from the scores. CRISPR/Cas9 target sites were predicted +genome-wide for the SP6-transcribed guide format, once without a constraint on the +first two bases and once each for guides starting with GG and with GA. These data were +produced by the Shawn Burgess laboratory at NHGRI and are distributed from + +their own site, which is also where questions about them are best directed. +
+ ++At UCSC the tracks were converted from the consortium's public track hub at + +trackhub2.genereg.net/DANIO-CODE with the script +danioCodeHubToRa.py, and the data files were copied from the same +server. The data themselves were not modified. The steps are documented in +our makeDoc. +
+ ++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=dcComparativeGenomics. +
+ ++For automated download and analysis, the annotations are stored in bigWig and bigBed files that +can be downloaded from +our +download server. The files are ZF_GC_CC_GF.danRer11.bw (phastCons), ZF_GC_CC_GF.danRer11.bb (conserved non-coding elements) and danRer11_sp6cas_N18_20.colored.bb, danRer11_sp6cas_GGN16_18NGG.colored.bb and danRer11_sp6cas_GAN16_18NGG.colored.bb (CRISPR targets). Individual regions or the whole genome annotation can be +obtained using our tool bigBedToBed, which can be compiled from the source code +or downloaded as a precompiled binary for your system. Instructions for downloading +source code and binaries can be found +here. +The tool can also be used to obtain features within a given range, for example +
+bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/ZF_GC_CC_GF.danRer11.bb \ + -chrom=chr1 -start=20000000 -end=20100000 stdout+ +
+The original data files, and the sample and protocol metadata behind them, are +available from the DANIO-CODE data coordination center at +danio-code.zfin.org and from +the consortium's track hub at + +trackhub2.genereg.net/DANIO-CODE. +
+ ++Thanks to the Shawn Burgess laboratory at NHGRI for producing and distributing these +data, and to the DANIO-CODE consortium for including them in their track hub. +