c2e552afa0d0574db2c2d93b51cd87b6484c4ddb jnavarr5 Fri Jun 13 15:59:17 2025 -0700 Adding links to the papers mentioned in the description for each track, refs #35703 diff --git src/hg/makeDb/trackDb/human/hg38/unusualcons.html src/hg/makeDb/trackDb/human/hg38/unusualcons.html index 746e69e7aba..0f7814454e3 100644 --- src/hg/makeDb/trackDb/human/hg38/unusualcons.html +++ src/hg/makeDb/trackDb/human/hg38/unusualcons.html @@ -1,54 +1,69 @@

Description

These tracks show regions of unusual conservation in human relative to other organisms:

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. + Elements with 100% identity in human/mouse/rat alignments. Many of these were tested in mice, + see the VISTA enhancers track in + the Regulation track group. (Bejerano et al, Science 2004)
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). + 2,649 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):
- 312 HARs from the Zoonomia Alignments (Keough et al. Science, 2023) + 312 HARs from the Zoonomia Alignments (Keough et al. Science, 2023)
Human Ancestor Quickly Evolved Regions (HAQERs):
- 1580 HAQERs from (Mangan Cell 2023) + 1,580 HAQERs from (Mangan Cell 2023)
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. + 583 regions (one not lifted) present in macaque and chimp, but no in humans. Since these are + sequences absent from the human genome, we show the 2bp around the deletion. + (McLean et al Nature 2011)
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. + 43,588 regions deleted in human but present in 11 vertebrates or primates. 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. (Xue et al, Science 2023)
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. + 4,552 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 conserved with chicken:
+ Non-coding elements > 200 bp long and 95% conserved between human and chicken. + (Dimitrieva and Bucher, NAR 2013)
UCNEBase: Elements paralogous to others:
- alignable with E<10^-4 to other chicken-conserved elements + 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 + Chicken-conserved elements within 0.5 Mb in both human and chicken.

Track	Count	Coverage in bp
Ultraconserved	481	126,007
UCNEBase Chicken