< patchesPsl | These tracks show the two types of patch sequences from the Genome Reference Consortium < patchesPsl | (GRC) patch releases:
< patchesPsl | < patchesPsl |< patchesPsl | This track shows alignments of fix patch sequences to < patchesPsl | main chromosome sequences in the reference genome assembly. < patchesPsl | When errors are corrected in the reference genome assembly, the < patchesPsl | Genome Reference Consortium < patchesPsl | (GRC) adds fix patch sequences containing the corrected regions. < patchesPsl | This strikes a balance between providing the most complete and correct genome < patchesPsl | sequence, while maintaining stable chromosome coordinates for the original assembly < patchesPsl | sequences. < patchesPsl |
< patchesPsl |< patchesPsl | Fix patches are often associated with incident reports displayed in the GRC Incidents < patchesPsl | track. < patchesPsl |
< patchesPsl | < patchesPsl |< patchesPsl | This track shows alignments of alternate locus (also known as "alternate haplotype") < patchesPsl | reference sequences to main chromosome sequences in the reference genome assembly. < patchesPsl | Some loci in the genome are highly variable, with sets of variants that tend < patchesPsl | to segregate into distinct haplotypes. < patchesPsl | Only one haplotype can be included in a reference assembly chromosome sequence. < patchesPsl | Instead of providing a separate complete chromosome sequence for each haplotype, < patchesPsl | which could cause confusion with divergent chromosome coordinates and < patchesPsl | ambiguity about which sequence is the official reference, the < patchesPsl | Genome Reference Consortium < patchesPsl | (GRC) adds alternate locus sequences, ranging from tens of thousands of bases < patchesPsl | up to low millions of bases in size, to represent the distinct haplotypes. < patchesPsl |
< patchesPsl | < patchesPsl |< patchesPsl | Both tracks follow the display conventions for < patchesPsl | < patchesPsl | PSL alignment tracks. < patchesPsl | Mismatching bases are highlighted in red. < patchesPsl | Several types of alignment gap may also be colored; < patchesPsl | for more information, see < patchesPsl | < patchesPsl | Alignment Insertion/Deletion Display Options. < patchesPsl |
< patchesPsl |< patchesPsl | By default, the tracks are only visible when there are items in the view window. < patchesPsl | This can be disabled by the checkbox Hide empty subtracks.
< patchesPsl | < patchesPsl |< patchesPsl | The alignments were provided by NCBI as GFF files and translated into the PSL < patchesPsl | representation for browser display by UCSC. < patchesPsl |
< patchesPsl | 28904,28909c28845,28851 < vistaEnhancersBb |Items appearing in blue (positive) indicate that a < vistaEnhancersBb | reproducible pattern was observed in the in vivo enhancer assay under at least one of the < vistaEnhancersBb | tested conditions. Items appearing in gray (negative) indicate < vistaEnhancersBb | that NO reproducible pattern was observed in the in vivo enhancer assay under any of the tested < vistaEnhancersBb | conditions. This does not exclude the possibility that this region is a reproducible enhancer active < vistaEnhancersBb | under different conditions, for example at an earlier or later timepoint in development.
--- > vistaEnhancersBb |Items appearing in red (positive) indicate that a reproducible > vistaEnhancersBb | pattern was observed in the in vivo enhancer assay. Items appearing in > vistaEnhancersBb | blue (negative) indicate that NO reproducible pattern was observed > vistaEnhancersBb | in the in vivo enhancer assay. Note that this annotation refers only to the single developmental > vistaEnhancersBb | timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this > vistaEnhancersBb | region is a reproducible enhancer active at earlier or later timepoints in development. > vistaEnhancersBb |
28912c28854 < vistaEnhancersBb | Excerpted from the Vista Enhancer vistaEnhancersBb | Excerpted from the Vista Enhancer vistaEnhancersBb | transgenic assays: vista-data bed files for
< vistaEnhancersBb | hg38 and mm10 into bigBed format using the bedToBigBed utility. The data for mm39 was lifted over
< vistaEnhancersBb | from mm10. The data for hg19 was lifted over from hg38.
Thanks to the Lawrence Berkeley National Laboratory for providing this data.
--- > vistaEnhancersBb |Thanks to the Lawrence Berkeley National Laboratory for providing this data
28968,28976d28910 < vistaEnhancersBb |< vistaEnhancersBb | Kosicki M, Baltoumas FA, Kelman G, Boverhof J, Ong Y, Cook LE, Dickel DE, Pavlopoulos GA, Pennacchio < vistaEnhancersBb | LA, Visel A. < vistaEnhancersBb | < vistaEnhancersBb | VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers. < vistaEnhancersBb | Nucleic Acids Res. 2025 Jan 6;53(D1):D324-D330. < vistaEnhancersBb | PMID: 39470740; PMC: PMC11701537 < vistaEnhancersBb |