SC UCNE

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



NV UCNE_ID S.cal Coordinate Browser Linkout element_size match_count mismatach_count
131 chr9:22194466..22194567 101 96 5
131 chr9:22194816..22194917 101 96 5
131 chr9:22197181..22197282 101 96 5
131 chr9:22195095..22195196 101 95 6
131 chr9:22195386..22195487 101 95 6
131 chr9:22232169..22232270 101 96 5
131 chr9:22240615..22240715 101 92 9
256 chrUn8:85846..85983 138 133 5
256 chrUn66:536737..536874 138 133 5
256 chrUn5:670351..670488 138 133 5
256 chrUn17:274783..274920 138 133 5
256 chr9:9895460..9895597 138 133 5
256 chr9:27890856..27890993 138 132 6
256 chr8:31138348..31138485 138 133 5
256 chr7:20170351..20170488 138 133 5
256 chr5:21862760..21862897 138 133 5
256 chr4:30768543..30768680 138 133 5
256 chr4:11998943..11999080 138 133 5
256 chr4:8125067..8125204 138 133 5
256 chr4:7892214..7892351 138 133 5
256 chr3:36067519..36067656 138 133 5
256 chr3:24026574..24026711 138 133 5
256 chr3:12930009..12930146 138 132 6
256 chr2:17746277..17746414 138 133 5
256 chr13:9983293..9983430 138 133 5
256 chrUn73:89748..89885 138 133 5
256 chrUn255:43077..43214 138 133 5
256 chrUn181:122602..122739 138 132 6
256 chr9:28170607..28170744 138 133 5
256 chr9:10798902..10799039 138 132 6
256 chr7:17881216..17881353 138 133 5
256 chr7:5392228..5392365 138 133 5
256 chr6:29241430..29241567 138 133 5
256 chr6:13232094..13232231 138 133 5
256 chr6:33020974..33021111 138 132 6
256 chr6:19880764..19880901 138 132 6
256 chr3:11966894..11967031 138 133 5
256 chr3:19459669..19459806 138 132 6
256 chr3:11048555..11048692 138 129 9
256 chr2:3168552..3168689 138 132 6
256 chr15:5417428..5417565 138 133 5
256 chr1:43276244..43276381 138 133 5
256 chr1:14363686..14363823 138 133 5
256 chr1:21646011..21646148 138 132 6
556 chrUn8:85846..85962 117 112 5
556 chrUn66:536737..536853 117 112 5
556 chrUn5:670351..670467 117 112 5
556 chrUn17:274783..274899 117 112 5
556 chr9:9895460..9895576 117 112 5
556 chr9:27890856..27890972 117 111 6
556 chr8:31138348..31138464 117 112 5
556 chr7:28250205..28250321 117 112 5
556 chr7:20170351..20170467 117 112 5
556 chr5:21862760..21862876 117 112 5
556 chr4:30768543..30768659 117 112 5
556 chr4:11998943..11999059 117 112 5
556 chr4:8125067..8125183 117 112 5
556 chr4:7892214..7892330 117 112 5
556 chr3:36067519..36067635 117 112 5
556 chr3:24026574..24026690 117 112 5
556 chr3:12930009..12930125 117 112 5
556 chr2:17746277..17746393 117 112 5
556 chr15:13489955..13490328 117 113 4
556 chr13:9983293..9983409 117 112 5
556 chrUn73:89769..89885 117 112 5
556 chrUn255:43098..43214 117 112 5
556 chrUn181:122623..122739 117 112 5
556 chr9:28170628..28170744 117 112 5
556 chr9:10798923..10799039 117 112 5
556 chr7:17881237..17881353 117 112 5
556 chr7:5392249..5392365 117 112 5
556 chr6:33020995..33021111 117 112 5
556 chr6:29241451..29241567 117 112 5
556 chr6:13232115..13232231 117 112 5
556 chr6:19880785..19880901 117 111 6
556 chr3:11966915..11967031 117 112 5
556 chr3:19459690..19459806 117 111 6
556 chr3:11048576..11048692 117 108 9
556 chr2:3168573..3168689 117 111 6
556 chr15:5417449..5417565 117 112 5
556 chr1:43276265..43276381 117 112 5
556 chr1:21646032..21646148 117 112 5
556 chr1:14363707..14363823 117 112 5
80 chrUn8:85863..85969 107 102 5
80 chrUn66:536754..536860 107 102 5
80 chrUn5:670368..670474 107 102 5
80 chrUn17:274800..274906 107 102 5
80 chr9:27890873..27890979 107 101 6
80 chr8:31138365..31138471 107 102 5
80 chr7:20170368..20170474 107 102 5
80 chr5:21862777..21862883 107 102 5
80 chr5:913160..913267 107 102 5
80 chr4:30768560..30768666 107 102 5
80 chr4:11998960..11999066 107 102 5
80 chr4:8125084..8125190 107 102 5
80 chr4:7892231..7892337 107 102 5
80 chr3:36067536..36067642 107 102 5
80 chr3:24026591..24026697 107 102 5
80 chr3:12930026..12930132 107 102 5
80 chr2:17746294..17746400 107 102 5
80 chr13:9983310..9983416 107 102 5
80 chrUn73:89762..89868 107 102 5
80 chrUn255:43091..43197 107 102 5
80 chrUn181:122616..122722 107 101 6
80 chr9:28170621..28170727 107 102 5
80 chr9:10798916..10799338 107 102 5
80 chr7:5392242..5392348 107 102 5
80 chr7:17881230..17881771 107 103 4
80 chr6:33020988..33021094 107 102 5
80 chr6:29241444..29241550 107 102 5
80 chr6:13232108..13232214 107 102 5
80 chr6:19880778..19880884 107 101 6
80 chr3:14227592..14228126 107 103 4
80 chr3:11966908..11967317 107 103 4
80 chr3:11048569..11048675 107 98 9
80 chr2:3168566..3168672 107 101 6
80 chr15:5417442..5417789 107 103 4
80 chr13:14894535..14894641 107 102 5
80 chr1:43276258..43276364 107 102 5
80 chr1:21646025..21646131 107 102 5
80 chr1:14363700..14363806 107 102 5
372 chrUn8:85852..85956 105 100 5
372 chrUn66:536743..536847 105 100 5
372 chrUn5:670357..670461 105 100 5
372 chrUn17:274789..274893 105 100 5
372 chr9:9895466..9895570 105 100 5
372 chr9:27890862..27890966 105 99 6
372 chr8:31138354..31138458 105 100 5
372 chr7:28250211..28250315 105 100 5
372 chr7:20170357..20170461 105 100 5
372 chr5:21862766..21862870 105 100 5
372 chr5:913149..913253 105 100 5
372 chr4:30768549..30768653 105 100 5
372 chr4:11998949..11999053 105 100 5
372 chr4:8125073..8125177 105 100 5
372 chr4:7892220..7892324 105 100 5
372 chr3:36067525..36067629 105 100 5
372 chr3:24026580..24026684 105 100 5
372 chr3:12930015..12930119 105 100 5
372 chr2:17746283..17746387 105 100 5
372 chr15:13489961..13490065 105 100 5
372 chr13:9983299..9983403 105 100 5
372 chrUn73:89775..89879 105 100 5
372 chrUn255:43104..43208 105 100 5
372 chrUn181:122629..122733 105 100 5
372 chr9:28170634..28170738 105 100 5
372 chr9:10798929..10799033 105 99 6
372 chr7:17881243..17881347 105 100 5
372 chr7:5392255..5392359 105 100 5
372 chr6:33021001..33021105 105 100 5
372 chr6:29241457..29241561 105 100 5
372 chr6:13232121..13232225 105 100 5
372 chr6:19880791..19880895 105 99 6
372 chr3:14227605..14227709 105 100 5
372 chr3:11966921..11967025 105 100 5
372 chr3:19459696..19459800 105 99 6
372 chr3:11048582..11048686 105 96 9
372 chr2:3168579..3168683 105 99 6
372 chr15:5417455..5417559 105 100 5
372 chr13:14894548..14894652 105 100 5
372 chr1:43276271..43276375 105 100 5
372 chr1:21646038..21646142 105 100 5
372 chr1:14363713..14363817 105 100 5
375 chr5:5687312..5687480 106 101 5
375 chr10:24915482..24915587 106 101 5
375 chr5:5704994..5705099 106 101 5
375 chr10:24933116..24933221 106 100 6
384 chr8:4324657..4324842 106 99 7
384 chr10:24915482..24915587 106 101 5
384 chr5:5704994..5705099 106 101 5
384 chr10:24933137..24933242 106 99 7
412 chr8:4324657..4324842 106 99 7
412 chr10:24915482..24915587 106 101 5
412 chr5:5704994..5705099 106 101 5
412 chr10:24933137..24933242 106 99 7
386 chr5:5687291..5687393 103 97 6
386 chr10:24915293..24915395 103 97 6
386 chr5:5704997..5705099 103 98 5
386 chr10:24933182..24933284 103 98 5
144 chr1:14725320..14725736 414 403 11
145 chr1:14725320..14725736 414 401 13
182 chr11:5212360..5212586 227 216 11
182 chr11:5039882..5040108 227 216 11
182 chr11:2067444..2067670 227 212 15
424 chr3:20408678..20408854 177 169 8
591 chr7:5389645..5389828 170 162 8
591 chr6:33018396..33018579 170 162 8
591 chr3:19456676..19456859 170 162 8
591 chr3:11964310..11964493 170 162 8
591 chr1:43273660..43273843 170 163 7
591 chr1:21641549..21641732 170 162 8
591 chrUn66:539261..539460 170 163 7
591 chrUn27:964943..965142 170 162 8
591 chr7:28259001..28259201 170 164 6
591 chr7:20172874..20173073 170 162 8
591 chr4:30772939..30773138 170 162 8
591 chr3:36070031..36070230 170 163 7
591 chr2:6381124..6381307 170 163 7
591 chr13:9985822..9986021 170 163 7
95 chr7:28968010..28968171 161 156 5
95 chr3:18288112..18288703 161 156 5
413 chr11:2075428..2075572 145 138 7
413 chr11:5037639..5037783 145 137 8
413 chr11:5210117..5210261 145 136 9
162 chr11:2075428..2075545 118 113 5
162 chr11:5037666..5037783 118 113 5
162 chr11:5210144..5210261 118 112 6
205 chr3:20408655..20408782 128 122 6
605 chr3:20408655..20408764 110 105 5
282 chr5:5704994..5705099 106 101 5
282 chr10:24933116..24933221 106 100 6
282 chrUn90:313013..313140 106 99 7
282 chr10:24915482..24915587 106 101 5
104 chr3:20408125..20408236 112 107 5
601 chr3:20408125..20408236 112 107 5
155 chr11:2075028..2075134 107 102 5
155 chr11:5210555..5210661 107 101 6
155 chr11:5038077..5038183 107 101 6
163 chr11:2075031..2075134 104 99 5
163 chr11:5210555..5210658 104 98 6
163 chr11:5038077..5038180 104 98 6
352 chr4:13405838..13405938 101 96 5
356 chr4:13405838..13405938 101 96 5
62 chr3:9520668..9520999 332 328 4
47 chr8:2821587..2821788 202 184 18
47 chr3:33277432..33277633 202 184 18
47 chr13:13584771..13584972 202 186 16
47 chr7:23591900..23592101 202 185 17
47 chr7:10880377..10880578 202 184 18
47 chr4:31830938..31831139 202 186 16
47 chr3:9519106..9519307 202 192 10
47 chr14:5545045..5545246 202 186 16
47 chr11:26912176..26912377 202 188 14
47 chr10:21177711..21177912 202 184 18
47 chr1:21408820..21409021 202 188 14
69 chr3:10584037..10584138 102 96 6
56 chr3:10582980..10583083 103 99 4
102 chr10:8244027..8244133 107 102 5
105 chr3:20406409..20406519 111 106 5
115 chrUn22:481140..481247 108 103 5
115 chr7:16665236..16665343 108 103 5
107 chr6:2834415..2834538 124 119 5
107 chr1:24950586..24950709 124 119 5
108 chr6:2835125..2835298 174 166 8
108 chr11:25988200..25988373 174 166 8
108 chr1:24949825..24949998 174 165 9
120 chrUn4:1451561..1451660 100 95 5
120 chr8:21084912..21085011 100 95 5
120 chr7:10453975..10454074 100 95 5
120 chr11:13932876..13932975 100 95 5
120 chr10:22994125..22994224 100 95 5
120 chr1:599077..599176 100 95 5
119 chrUn4:1452138..1452314 177 169 8
119 chr8:21085489..21085665 177 168 9
119 chr7:10454554..10454730 177 169 8
119 chr11:13932223..13932399 177 169 8
119 chr10:22993510..22993686 177 169 8
119 chr1:598423..598599 177 169 8
206 chr3:20408125..20408236 112 107 5
209 chr11:2074856..2075365 107 102 5
209 chrUn84:215894..216403 107 103 4
209 chr8:23628497..23629006 107 103 4
209 chr11:5210324..5210430 107 97 10
158 chr11:2075403..2075515 113 108 5
158 chr11:5037696..5037808 113 108 5
158 chr11:5210174..5210286 113 107 6
231 chrUn73:87526..87634 109 103 6
231 chr9:10796683..10796791 109 103 6
231 chr6:33018763..33018871 109 103 6
231 chr6:19878546..19878654 109 103 6
231 chr5:11217525..11217633 109 103 6
231 chr4:29356146..29356254 109 103 6
231 chr3:11964677..11964785 109 103 6
231 chr3:19457043..19457557 109 103 6
231 chr15:5415212..5415320 109 103 6
231 chr1:43274027..43274135 109 103 6
231 chr1:21643795..21643903 109 103 6
231 chrUn66:538985..539093 109 103 6
231 chr7:20172598..20172706 109 102 7
231 chr4:30770769..30770877 109 103 6
231 chr4:8127312..8127420 109 103 6
231 chr4:7894460..7894568 109 103 6
231 chr3:36069756..36069864 109 103 6
231 chr2:6380831..6380939 109 104 5
231 chr2:17748521..17748629 109 101 8
231 chr13:9985546..9985654 109 103 6
360 chr4:20849127..20849237 110 106 4
359 chrUn54:585201..585305 105 100 5
359 chr4:17082847..17082951 105 100 5
361 chr4:19941813..19941949 137 131 6
348 chrUn146:169748..169857 110 104 6
348 chr7:5368740..5368849 110 105 5
348 chr3:19454077..19454186 110 105 5
348 chr15:5414387..5414496 110 105 5
348 chrUn27:967690..967799 110 104 6
348 chr3:36072778..36072887 110 105 5
342 chr7:19921885..19922002 118 113 5
342 chr1:24948910..24949027 118 113 5
342 chr6:2836096..2836213 118 113 5
342 chr12:4324362..4324479 118 113 5
342 chr11:25990995..25991112 118 113 5
339 chr7:19922113..19922218 106 100 6
339 chr1:24949138..24949243 106 101 5
339 chr6:2835880..2835985 106 100 6
339 chr12:4324146..4324251 106 101 5
339 chr11:25990779..25990884 106 100 6
341 chr1:24950586..24950753 168 163 5
341 chr6:2834371..2834538 168 163 5
344 chrUn53:641479..641579 101 95 6
344 chrUn47:68242..68342 101 95 6
344 chr6:16633771..16633871 101 96 5
344 chr12:13317519..13317619 101 96 5
416 chrUn84:215987..216092 106 96 10
416 chr11:5210417..5210522 106 101 5
416 chr11:5037939..5038044 106 101 5
446 chr8:31195004..31195128 125 123 2
446 chrUn16:1120074..1120198 125 125 0
446 chrUn16:1118643..1118767 125 125 0
446 chr9:6337525..6337649 125 125 0
446 chr9:6335966..6336090 125 124 1
448 chrUn9:1048276..1048379 104 99 5
448 chr8:25626076..25626179 104 99 5
440 chrUn84:270075..270177 103 98 5
440 chr8:23686134..23686236 103 98 5
438 chr8:28024701..28024809 109 104 5
441 chr8:26966089..26966202 114 109 5
425 chr11:13882984..13883084 101 91 10
425 chr11:11243655..11243755 101 91 10
425 chr5:6461517..6461617 101 96 5
465 chrUn8:86977..87103 127 122 5
465 chrUn66:538630..538756 127 121 6
465 chr4:30770414..30770541 127 123 4
465 chr4:8126958..8127084 127 122 5
465 chr4:7894104..7894231 127 122 5
465 chr3:36069410..36069536 127 122 5
465 chr2:17748167..17748293 127 122 5
465 chr2:6380477..6380603 127 122 5
465 chr13:9985191..9985317 127 122 5
465 chrUn73:87863..87989 127 122 5
465 chr9:10797019..10797145 127 122 5
465 chr7:17879334..17879460 127 122 5
465 chr6:19878883..19879009 127 122 5
465 chr6:33019098..33019224 127 121 6
465 chr4:29356483..29356609 127 122 5
465 chr3:19457788..19457914 127 122 5
465 chr3:11965013..11965139 127 121 6
465 chr15:5415549..5415675 127 122 5
465 chr1:43274364..43274490 127 122 5
465 chr1:21644131..21644257 127 122 5
454 chrUn82:192008..192115 108 99 9
454 chrUn2:467471..468298 108 104 4
454 chrUn2:466742..469457 108 104 4
454 chrUn2:470179..470536 108 105 3
454 chrUn2:466382..466879 108 103 5
454 chrUn2:470329..470976 108 105 3
454 chrUn2:467151..468078 108 103 5
454 chrUn2:469360..470146 108 105 3
454 chrUn2:466522..470736 108 101 7
454 chr9:1504093..1506121 108 104 4
454 chr9:1504817..1505273 108 105 3
454 chr9:1505096..1505632 108 105 3
454 chr9:1501915..1502877 108 105 3
454 chr9:1503087..1503333 108 104 4
454 chr9:24460705..24462030 108 103 5
454 chr9:24462359..24462585 108 104 4
454 chr9:1503555..1503911 108 104 4
454 chr9:1504451..1504628 108 105 3
454 chr9:1505246..1505452 108 101 7
454 chr9:1499994..1502479 108 104 4
454 chr8:11896881..11897027 108 105 3
454 chr8:11894974..11895171 108 104 4
454 chr8:11895821..11897534 108 105 3
454 chr8:11894745..11895421 108 104 4
454 chr8:11895979..11896741 108 104 4
454 chr7:32172185..32172620 108 103 5
454 chr7:32172991..32173308 108 103 5
454 chr7:32174031..32174978 108 103 5
454 chr7:32171545..32171821 108 102 6
454 chr7:32173591..32173808 108 103 5
454 chr7:32174641..32174868 108 101 7
454 chr7:32174741..32175098 108 105 3
454 chr7:32173321..32173778 108 103 5
454 chr7:32171017..32171414 108 106 2
454 chr7:32172344..32175068 108 103 5
454 chr5:2414929..2415176 108 103 5
454 chr5:2417753..2418180 108 103 5
454 chr5:12949183..12950509 108 104 4
454 chr5:12882374..12882719 108 104 4
454 chr5:12881723..12882789 108 102 6
454 chr5:12949203..12950726 108 104 4
454 chr5:12950260..12951294 108 102 6
454 chr5:2417603..2417720 108 100 8
454 chr4:18165359..18170850 108 106 2
454 chr4:18171247..18171793 108 103 5
454 chr4:18169492..18171603 108 103 5
454 chr4:18165686..18167978 108 105 3
454 chr4:14312736..14313315 108 104 4
454 chr4:14312564..14314548 108 102 6
454 chr4:18165013..18165307 108 105 3
454 chr4:14311835..14314488 108 104 4
454 chr4:18168727..18168962 108 100 8
454 chr4:14311085..14311703 108 104 4
454 chr4:14311825..14312703 108 104 4
454 chr3:15493701..15494058 108 105 3
454 chr3:15493371..15493758 108 101 7
454 chr3:26019140..26019417 108 104 4
454 chr3:34371044..34371682 108 100 8
454 chr3:38137494..38137779 108 98 10
454 chr12:16581140..16582166 108 104 4
454 chr12:16585853..16586020 108 103 5
454 chr12:16582069..16582186 108 102 6
454 chr12:16583720..16585294 108 103 5
454 chr12:16585376..16587486 108 105 3
454 chr12:16579722..16580184 108 102 6
454 chr12:16584396..16584888 108 102 6
454 chr12:16583336..16586749 108 103 5
454 chr12:16577875..16577982 108 99 9
454 chr12:16580416..16580869 108 105 3
454 chr1:15783294..15783870 108 104 4
454 chr1:15783773..15784360 108 104 4
454 chr1:15785202..15785738 108 102 6
454 chr1:15784702..15786297 108 105 3
454 chr1:15786410..15786597 108 101 7
454 chr1:15722429..15723056 108 104 4
454 chr1:15782159..15782277 108 101 7
454 chr1:15783314..15784719 108 103 5
454 chrUn2:455980..456207 108 104 4
454 chrUn2:452971..453078 108 101 7
454 chrUn2:453701..453818 108 103 5
454 chrUn2:454282..454779 108 103 5
454 chrUn2:453401..454309 108 103 5
454 chrUn2:452911..453248 108 104 4
454 chrUn2:452841..453338 108 104 4
454 chr9:24443671..24444031 108 102 6
454 chr9:1043738..1043895 108 100 8
454 chr9:1043399..1043666 108 103 5
454 chr9:24444171..24445120 108 104 4
454 chr9:24445054..24445420 108 99 9
454 chr9:24446176..24446727 108 103 5
454 chr9:24442842..24443149 108 104 4
454 chr8:11886692..11887786 108 104 4
454 chr8:11888016..11888332 108 102 6
454 chr8:11885568..11887249 108 104 4
454 chr8:11885538..11886132 108 103 5
454 chr8:11885976..11888043 108 103 5
454 chr8:11888215..11888914 108 102 6
454 chr7:32166400..32166866 108 105 3
454 chr7:32163632..32163829 108 105 3
454 chr7:32167359..32167616 108 103 5
454 chr7:32167679..32168013 108 100 8
454 chr7:32164999..32165392 108 104 4
454 chr7:32163872..32165849 108 99 9
454 chr5:2407189..2408122 108 104 4
454 chr5:2404750..2406988 108 106 2
454 chr5:2404600..2404717 108 102 6
454 chr5:2405808..2407901 108 104 4
454 chr5:12847691..12847878 108 104 4
454 chr5:12854520..12854647 108 104 4
454 chr5:12855210..12855357 108 104 4
454 chr5:2404630..2404956 108 102 6
454 chr5:12855240..12855947 108 103 5
454 chr5:2404043..2404209 108 103 5
454 chr5:12852708..12852855 108 101 7
454 chr5:12855860..12856079 108 103 5
454 chr5:12851522..12852019 108 103 5
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