53da311c2aa0cff3f0feee6d90e52ff7e0ec6ca5
jnavarr5
Fri Jun 13 14:59:48 2025 -0700
Making the track name bold and moving the definition to a new line to make the section less cluttered. Changing < and > to HTML entities, refs #35703
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Description
These tracks show regions of unusual conservation in human relative to other organisms:
- - Ultraconserved elements (UCE aka ultras):
+
- Ultraconserved elements (UCE aka ultras):
Elements with 100% identity in human/mouse/rat alignments, from (Bejerano et al, Science 2004).
Many of these were tested in mice, see the VISTA enhancers track in the Regulation track group.
- - Human Accelerated Regions (HARs):
+
- Human Accelerated Regions (HARs):
2649 regions conserved throughout vertebrate evolution but strikingly different in humans (Pollard et al, Nature 2006).
This extended list was collected by the Katie Pollard lab from various publications (Capra et al. PTRSB 2013).
- - High-confidence Zoonomia Human Accelerated Regions (HARs):
+
- High-confidence Zoonomia Human Accelerated Regions (HARs):
312 HARs from the Zoonomia Alignments (Keough et al. Science, 2023)
- - Human Ancestor Quickly Evolved Regions (HAQERs):
+
- Human Ancestor Quickly Evolved Regions (HAQERs):
1580 HAQERs from (Mangan Cell 2023)
- - Human-specific long deletions (hCondels) between human, macaque and chimpanzee:
+
- Human-specific long deletions (hCondels) between human, macaque and chimpanzee:
583 regions (one not lifted) present in macaque and chimp, but no in humans. (McLean et al Nature 2011)
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:
+
- 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
+
- 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):
+
- 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:
+
- 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
Track |
Count |
Coverage in bp |
Ultraconserved |
481 |
126,007 |