NV UCNE

Nematostella vectensis Ultra Conserved Noncoding Elements


Excerpt from Zimmerman et. al., 2021

Genomic Distribution of Ultraconserved Non-coding Elements

Longer stretches of unusually highly conserved non-coding genomic regions have been studied thoroughly in vertebrates with varying methodologies. These ultraconserved non-coding elements (UCNEs) are generally posited to be cis-regulatory regions, but the precise mechanistic requirement for such high conservation is not fully understood. While some previous studies have argued that the degree of conservation observed in UCNEs is specific to vertebrates, a more recent study has asserted that UCNEs are present in smaller numbers within Drosophila. We were therefore interested to find out how many, and to what extent, UCNEs are present in Edwardsiidae. We adopted criteria previously used to detect UCNEs between chicken and humans and found 145 regions in the Nematostella genome that were highly conserved with Scolanthus. 116 of these regions fell into 37 syntenic clusters of at most 500 kb intervening gaps, and the remaining 29 were singletons. Several such clusters were close to NK paralogs, such as one containing 12 UCNEs and spanning 70 kb surrounding the NK3-4 cluster on chromosome 5 and three UCNEs upstream of the NK2.2 cluster on chromosome 2, a pattern previously reported in vertebrates. Additionally, we detected a single UCNE neighboring the PaxC gene. While Pax-associated UCNEs have been previously reported in vertebrates, this neural developmental gene appears to have arisen from a cnidarian-specific duplication, implying that the accompanying UCNE also arose independently. On the other hand, no UCNEs are found near the edwardsiid Irx gene, despite their ubiquity among Bilateria. Likewise, our stringent criteria did not detect the previously reported UCNE at the 3’end of the SoxB2 gene, as previously reported, suggesting that more relaxed parameters might reveal additional conserved elements shared between more distantly related species.




Nematostella vectensis UCNE were aligned to the genome using BLAT. Locations of matches, element size, match and mismatch counts are listed below. A table of alignments of these same elements to Scolanthus callimorphuscan is also available.


NV UCNE_ID Coordinate Browser Linkout element_size match_count mismatach_count
127 chr12:1597906..1598038 133 133 0
127 chr12:1596694..1596828 133 133 0
127 chr12:1598105..1598239 133 133 0
127 chr12:1598912..1599046 133 133 0
127 chr12:1607226..1607360 133 133 0
127 chr12:1609254..1609388 133 133 0
127 chr12:1612097..1612231 133 133 0
128 chr12:1597298..1597423 126 126 0
128 chr12:1596694..1596827 126 126 0
128 chr12:1597906..1598037 126 126 0
128 chr12:1598105..1598238 126 126 0
128 chr12:1598912..1599045 126 126 0
128 chr12:1607226..1607359 126 126 0
128 chr12:1609254..1609387 126 126 0
128 chr12:1612097..1612230 126 126 0
129 chr12:1598511..1598636 126 126 0
130 chr12:1602557..1602681 125 125 0
130 chr12:1604586..1604710 125 125 0
130 chr12:1606006..1606130 125 125 0
130 chr12:1608035..1608159 125 125 0
130 chr12:1610471..1610595 125 125 0
130 chr12:1611284..1611408 125 125 0
130 chr12:1613308..1613432 125 125 0
130 chr12:1614119..1614243 125 125 0
130 chr12:1617168..1617292 125 125 0
130 chr12:1620421..1620545 125 125 0
130 chr12:1624080..1624204 125 125 0
131 chr12:8107291..8107391 101 101 0
256 chr14:9499521..9499658 138 138 0
556 chr7:2547808..2547924 117 117 0
80 chr1:1918153..1918259 107 107 0
372 chr2:434910..435014 105 105 0
375 chr3:6641329..6641434 106 106 0
384 chr3:6641203..6641308 106 106 0
384 chr3:6642337..6642442 106 106 0
384 chr3:6642253..6642358 106 106 0
412 chr3:6641203..6641308 106 106 0
412 chr3:6642337..6642442 106 106 0
412 chr3:6642253..6642358 106 106 0
386 chr3:6642757..6642859 103 103 0
144 chr13:11859965..11860378 414 414 0
145 chr13:11877626..11878039 414 414 0
146 chr13:11844553..11844935 383 383 0
182 chr13:12421184..12421410 227 227 0
420 chr3:1314964..1315127 164 164 0
424 chr3:16137010..16137186 177 177 0
602 chr8:12808115..12808238 124 124 0
602 chr13:9134712..9134835 124 124 0
591 chr8:6123654..6123823 170 170 0
261 chr14:1726275..1726374 100 100 0
95 chr1:3009743..3009903 161 161 0
334 chr15:5601950..5602090 141 141 0
413 chr3:1317396..1317540 145 145 0
162 chr13:5169894..5170011 118 118 0
205 chr13:9134694..9134821 128 128 0
605 chr8:141892..142001 110 110 0
605 chr13:9134694..9134803 110 110 0
274 chr15:4492770..4492894 125 125 0
282 chr15:4492851..4492956 106 106 0
282 chr15:4492725..4492830 106 106 0
282 chr15:4492434..4492539 106 106 0
255 chr14:1726493..1726616 124 124 0
614 chr8:6123880..6123979 100 100 0
579 chr8:3953929..3954044 116 116 0
579 chr8:3941150..3941265 116 116 0
580 chr8:3953929..3954044 116 116 0
580 chr8:3941150..3941265 116 116 0
104 chr8:12808670..12808781 112 112 0
104 chr10:5730539..5730650 112 112 0
104 chr13:9128809..9128920 112 112 0
104 chr1:21509123..21509234 112 112 0
601 chr8:12808670..12808781 112 112 0
601 chr10:5730539..5730650 112 112 0
601 chr13:9128809..9128920 112 112 0
601 chr1:21509123..21509234 112 112 0
155 chr13:5164492..5164598 107 107 0
163 chr13:5169497..5169600 104 104 0
352 chr2:7147992..7148092 101 101 0
352 chr2:7131583..7131683 101 101 0
356 chr2:7147992..7148092 101 101 0
356 chr2:7131583..7131683 101 101 0
58 chr1:2674734..2674836 103 103 0
63 chr1:6556975..6557089 115 115 0
65 chr1:6915340..6915472 133 133 0
62 chr1:11450811..11451142 332 332 0
48 chr1:11451385..11452407 1023 1023 0
47 chr1:11452503..11452704 202 202 0
44 chr1:11453286..11453482 197 197 0
72 chr1:11453490..11453678 189 189 0
40 chr1:11454274..11454935 662 662 0
25 chr1:14158639..14158738 100 100 0
64 chr1:16609080..16609305 226 226 0
69 chr1:16619314..16619415 102 102 0
57 chr1:16620136..16620238 103 103 0
56 chr1:16620373..16620475 103 103 0
55 chr1:16620578..16620715 138 138 0
102 chr10:2915821..2915927 107 107 0
101 chr10:2916013..2916180 168 168 0
105 chr10:5732427..5732537 111 111 0
105 chr8:139492..139602 111 111 0
103 chr10:11633994..11634096 103 103 0
115 chr11:770573..770680 108 108 0
118 chr11:2194006..2194112 107 107 0
107 chr11:7764733..7764856 124 124 0
108 chr11:7765400..7765573 174 174 0
120 chr12:1415272..1415371 100 100 0
119 chr12:1415845..1416021 177 177 0
121 chr12:2855377..2855477 101 101 0
126 chr12:5453233..5453379 147 147 0
132 chr12:13218564..13218668 105 105 0
206 chr13:9128809..9128920 112 112 0
206 chr1:21509123..21509234 112 112 0
206 chr8:12808670..12808781 112 112 0
206 chr10:5730539..5730650 112 112 0
209 chr13:12423163..12423269 107 107 0
158 chr13:12423307..12423419 113 113 0
231 chr14:1726637..1726745 109 109 0
335 chr15:5443837..5443960 124 124 0
360 chr2:1577594..1577703 110 110 0
359 chr2:2671884..2671988 105 105 0
355 chr2:4194736..4194839 104 104 0
361 chr2:4524575..4524711 137 137 0
354 chr2:5093897..5094000 104 104 0
353 chr2:5094095..5094207 113 113 0
362 chr2:5549081..5549188 108 108 0
358 chr2:8084861..8084970 110 110 0
357 chr2:8085254..8085400 147 147 0
348 chr2:9143787..9143896 110 110 0
366 chr2:16246713..16246812 100 100 0
363 chr2:17866987..17867104 118 118 0
342 chr2:19325851..19325968 118 118 0
339 chr2:19326079..19326184 106 106 0
367 chr2:19326774..19326976 203 203 0
341 chr2:19327520..19327687 168 168 0
344 chr2:20080063..20080163 101 101 0
364 chr2:21017063..21017161 99 99 0
416 chr3:1317135..1317240 106 106 0
446 chr3:4317307..4317431 125 125 0
446 chr3:7626593..7626717 125 125 0
439 chr3:4601105..4601203 99 99 0
448 chr3:4601479..4601582 104 104 0
450 chr3:7626584..7626718 135 135 0
440 chr3:7851974..7852076 103 103 0
438 chr3:9461707..9461815 109 109 0
442 chr3:10056462..10056588 127 127 0
441 chr3:12460897..12461010 114 114 0
434 chr3:12469060..12469246 187 187 0
425 chr3:20719251..20719351 101 101 0
465 chr4:6681078..6681204 127 127 0
454 chr4:6694741..6694848 108 108 0
477 chr4:8883225..8883380 156 156 0
488 chr5:3734577..3734678 102 102 0
496 chr5:3832334..3832444 111 111 0
501 chr5:4725175..4725276 102 102 0
498 chr5:5037968..5038082 115 115 0
502 chr5:5922474..5922573 100 100 0
509 chr5:5993178..5993278 101 101 0
510 chr5:7082627..7082727 101 101 0
494 chr5:7235708..7235817 110 110 0
506 chr5:11856370..11856496 127 127 0
508 chr5:11859239..11859346 108 108 0
497 chr5:11859972..11860071 100 100 0
487 chr5:11862683..11862817 135 135 0
486 chr5:11862931..11863041 111 111 0
485 chr5:11863459..11863609 151 151 0
484 chr5:11863613..11863779 167 167 0
483 chr5:11863784..11863887 104 104 0
500 chr5:11864548..11864648 101 101 0
499 chr5:11864651..11864755 105 105 0
493 chr5:11926991..11927146 156 156 0
492 chr5:11927149..11927249 101 101 0
505 chr5:13283626..13283726 101 101 0
505 chr5:13268645..13268745 101 101 0
482 chr5:15413309..15413410 102 102 0
515 chr6:3486962..3487082 121 121 0
511 chr6:5331549..5331652 104 104 0
560 chr7:2549713..2549818 106 106 0
539 chr7:2549944..2550047 104 104 0
604 chr8:142024..142133 110 110 0
604 chr8:12808015..12808124 110 110 0
584 chr8:1236650..1236749 100 100 0
583 chr8:2460927..2461028 102 102 0
627 chr8:6109325..6109459 135 135 0
640 chr8:6110619..6110754 136 136 0
607 chr8:6110884..6110997 114 114 0
631 chr8:6124122..6124221 100 100 0
618 chr8:6124466..6124578 113 113 0
577 chr8:12072455..12072556 102 102 0
603 chr8:12808012..12808112 101 101 0
603 chr8:142036..142136 101 101 0
576 chr8:15293124..15293257 134 134 0
575 chr8:15293336..15293452 117 117 0
668 chr9:3005492..3005595 104 104 0
663 chr9:11833629..11833758 130 130 0
663 chr9:11821525..11821654 130 130 0