a442752cfb1738add6158966133902bdc47e69d0 max Sun May 25 14:11:39 2025 -0700 adding ucnebase to unusual conservation track, refs #35703 diff --git src/hg/makeDb/trackDb/human/hg38/unusualcons.html src/hg/makeDb/trackDb/human/hg38/unusualcons.html index 9959948f4b5..6812a31c904 100644 --- src/hg/makeDb/trackDb/human/hg38/unusualcons.html +++ src/hg/makeDb/trackDb/human/hg38/unusualcons.html @@ -17,43 +17,64 @@ Since these are sequences absent from the human genome, we show the 2bp around the deletion.
  • Short hCondels < 40bp in primates and up to 11 vertebrates: 43588 regions deleted in human but present in 11 vertebrates or primates from (Xue et al, Science 2023). These regions were tested in an MPRA screen, the MPRA results are in the track and shown when clicking an element. Since the track is showing MPRA results and the position of deletions, what is shown in the track are regions +-100bp around the deletion site on the human genome, not just the two basepairs flanking the site of the deletion.
  • Zoonomia Ultraconserved elements (zooUCEs): 4552 Ultraconserved elements identified from the 241-mammals genome alignment. All regions >=20bp where at least 235 species aligned and all aligning species are fixed for the same base at every position. 20-190 bp.
  • Zoonomia: Runs of contiguous constraint (RoCCs): All genomic regions where contiguous bases have phyloP score > 2.270 (5% FDR) and are therefore under high constraint. Regions separated by a single base with phyloP < 2.270 were merged. N = 595,535; 20-1,359 bp.
  • Zoonomia: Unannotated Intergenic Constrained Regions (UNICORNs): Non-coding regions of the genome that lack annotation in ENCODE3 but show high evolutionary constraint, suggesting function. Positions with phyloP > 2.270 (5% FDR) within 5bp of each other are grouped into UNICORNs. N = 424,180; 11 - 1,325 bp. +
  • UCNEBase: Elements conserved with chicken from (Dimitrieva and Bucher, NAR 2013): + non-coding elements > 200 bp long and 95% conserved between human and chicken +
  • UCNEBase: Elements paralogous to others: + alignable with E<10^-4 to other chicken-conserved elements +
  • UCNEBase UGRBs: Ultra-conserved genomic regulatory blocks: + chicken-conserved elements within 0.5 Mb in both human and chicken + + + + + + + + + + + + + + + @@ -178,15 +199,24 @@ PMID: 21390129; PMC: PMC3071156

    Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Zoonomia Consortium†, Lindblad-Toh K et al. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science. 2023 Apr 28;380(6643):eabn2253. PMID: 37104592; PMC: PMC10202372

    +

    +Dimitrieva S, Bucher P. + +UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. +Nucleic Acids Res. 2013 Jan;41(Database issue):D101-9. +PMID: 23193254; PMC: PMC3531063 +

    +
    Track Count Coverage in bp
    Ultraconserved 481 126,007
    UCNEBase Chicken43511,415,142
    UCNEBase Paralogs987215,800
    UCNEBase UGRBs239199,269,634
    Zoo Ultracons. 4552 131,661
    HARs 2647 681,420
    ZooHARs 312 49,173