Electronic Supplement

Ultraconserved Elements in the Human Genome.
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D.
Science, 304(5675), pp. 1321-1325 (2004). free reprint pubmed

Paper Abstract

There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.

Figure 1

Chromosomal distribution of intervals:

chr1 ps pdf	chr2 ps pdf	chr3 ps pdf	chr4 ps pdf	chr5 ps pdf	chr6 ps pdf	chr7 ps pdf	chr8 ps pdf
chr9 ps pdf	chr10 ps pdf	chr11 ps pdf	chr12 ps pdf	chr13 ps pdf	chr14 ps pdf	chr15 ps pdf	chr16 ps pdf
chr17 ps pdf	chr18 ps pdf	chr19 ps pdf	chr20 ps pdf	chr21 ps pdf	chr22 ps pdf	chrX ps pdf	chrY ps pdf

Note that you will probably need to scroll down when the figure first shows.
See Figure 1 and text for further details.

Raw Sequences

Download the Watson strand DNA of all the ultra conserved elements.

Build 35 (hg17) Custom Track

Click here to add a custom track of ultraconserved elements to the UCSC genome browser display of Human Build 35 (hg17).

Supplementary Table 1

In column type 'e' is exonic, 'n' is non-exonic and 'p' is possibly exonic.
Background colors for 'e' and 'n' mimic those of the tick marks of Figure 1.
In right half of table, columns contain the number of element bases overlapping the respective feature.
Build 34 (hg16) coords are of the element itself, yet the link will open a display three times its length, to show genomic context.
Consult text for full legend.

ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.1 p 207 chr1:10307243-10307449 65151 DFFA PEX14 AK130996 99286 0 0 0 66 0 0 207 0 0 0 0.0988 207 196 0 0
uc.2 n 207 chr1:10442089-10442295 34690 AK130996 FLJ20321 FLJ37118 273783 0 0 0 0 0 0 207 0 0 0 0.8707 189 189 0 0
uc.3 p 225 chr1:10460711-10460935 53312 AK130996 FLJ20321 FLJ37118 255143 0 0 0 222 0 0 225 0 0 0 0.1818 225 212 0 0
uc.4 n 359 chr1:10467795-10468153 4286 FLJ20321 \N FLJ37118 247925 0 0 0 0 0 0 0 359 0 0 0.4531 359 347 359 287
uc.5 n 214 chr1:10490897-10491110 27388 FLJ20321 \N FLJ37118 224968 0 0 0 0 0 0 0 0 0 214 0.0574 213 212 200 179
uc.6 p 301 chr1:10504667-10504967 41158 FLJ20321 \N FLJ37118 211111 0 0 0 301 0 0 0 0 0 301 0.2363 301 288 279 237
uc.7 p 256 chr1:10545679-10545934 82170 FLJ20321 \N FLJ37118 170144 0 0 0 235 0 0 0 0 0 256 0.2663 256 247 0 0
uc.8 n 216 chr1:10561364-10561579 97855 FLJ20321 \N FLJ37118 154499 0 0 0 0 0 0 0 0 0 216 0.2285 207 202 207 172
uc.9 n 202 chr1:10634956-10635157 171447 FLJ20321 \N FLJ37118 80921 0 0 0 0 0 0 0 0 0 202 0.0222 202 195 0 0
uc.10 n 275 chr1:10675120-10675394 211611 FLJ20321 \N FLJ37118 40684 0 0 0 0 0 0 0 0 0 275 0.0177 275 273 275 250
uc.12 p 201 chr1:35077889-35078089 68766 FLJ23151 SFPQ ZNF262 140539 0 0 0 201 0 0 201 0 0 0 0.6008 201 189 201 110
uc.13 e 237 chr1:35786852-35787088 36769 EIF2C4 EIF2C1 EIF2C3 36892 137 137 197 199 0 137 100 0 0 0 0.1805 201 162 160 134
uc.14 p 213 chr1:37908298-37908510 5531 CGI-94 \N POU3F1 15061 0 0 0 10 0 0 0 0 213 0 0.3971 213 185 0 0
uc.15 n 233 chr1:37974370-37974602 48625 POU3F1 \N RRAGC 742565 0 0 0 0 0 0 0 0 0 233 0.4661 233 229 197 183
uc.16 p 211 chr1:38041493-38041703 115748 POU3F1 \N RRAGC 675464 0 0 0 24 0 0 0 0 0 211 0.0929 211 180 0 0
uc.17 n 237 chr1:38215445-38215681 289700 POU3F1 \N RRAGC 501486 0 0 0 0 0 0 0 0 0 237 0.3543 237 171 0 0
uc.18 n 238 chr1:44128955-44129192 29316 DMAP1 PRNPIP FLJ10597 382114 0 0 0 0 0 0 238 0 0 0 0.214 224 209 0 0
uc.19 n 256 chr1:44403606-44403861 169431 PRNPIP \N FLJ10597 107445 0 0 0 0 0 0 0 0 0 256 0.8574 256 244 0 0
uc.20 p 269 chr1:44415666-44415934 181491 PRNPIP \N FLJ10597 95372 0 0 0 25 0 0 0 0 0 269 0.7435 269 239 0 0
uc.21 n 235 chr1:48482903-48483137 175140 SPATA6 FLJ14442 FLJ11588 80321 0 0 0 0 0 0 235 0 0 0 0.1828 235 223 0 0
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.22 n 308 chr1:50376149-50376456 119188 DMRTA2 FAF1 LOC51336 413691 0 0 0 0 0 0 308 0 0 0 0.1317 308 300 284 179
uc.23 n 229 chr1:50405695-50405923 148734 DMRTA2 FAF1 LOC51336 384224 0 0 0 0 0 0 229 0 0 0 0.025 229 226 152 112
uc.24 n 336 chr1:50469063-50469398 212102 DMRTA2 FAF1 LOC51336 320749 0 0 0 0 0 0 336 0 0 0 0.2441 336 331 0 0
uc.25 n 235 chr1:50535952-50536186 278991 DMRTA2 FAF1 LOC51336 253961 0 0 0 0 0 0 235 0 0 0 0.162 235 233 77 54
uc.26 n 212 chr1:62739563-62739774 38822 AUTL1 \N FOXD3 419268 0 0 0 0 0 0 0 0 0 212 0.2032 212 212 212 191
uc.27 n 290 chr1:62739797-62740086 39056 AUTL1 \N FOXD3 418956 0 0 0 0 0 0 0 0 0 290 0.0501 290 290 290 273
uc.28 e 355 chr1:70066629-70066983 25453 FLJ20331 SFRS11 DKFZP566D1346 29852 355 181 355 355 355 0 355 0 0 0 0.0883 355 340 167 132
uc.29 n 219 chr1:87244976-87245194 11120 LMO4 \N AF118089 1371952 0 0 0 0 0 0 0 0 0 219 0.0045 219 219 219 209
uc.30 n 243 chr1:87451593-87451835 217737 LMO4 \N AF118089 1165311 0 0 0 0 0 0 0 0 0 243 0.2468 243 239 0 0
uc.31 n 253 chr1:88395168-88395420 1161312 LMO4 \N AF118089 221726 0 0 0 0 0 0 0 0 0 253 0.0118 168 165 103 92
uc.33 e 312 chr1:96743538-96743849 9890 BC030757 PTBP2 DPYD 271253 34 36 34 269 0 34 312 0 0 0 0.3978 252 251 201 124
uc.34 e 208 chr1:96751973-96752180 18325 BC030757 PTBP2 DPYD 262922 176 0 208 208 176 0 0 0 32 0 0.0164 208 204 62 31
uc.35 p 205 chr1:97465205-97465409 713056 PTBP2 DPYD AK092728 506426 0 0 0 165 0 0 205 0 0 0 0.2712 205 186 0 0
uc.36 p 264 chr1:108587040-108587303 36279 FLJ30525 FLJ10330 FLJ35838 24296 0 0 158 264 0 0 264 0 0 0 0.1423 264 258 0 0
uc.37 e 202 chr1:114578780-114578981 41876 AMPD1 D1S155E FLJ21168 35142 93 102 202 202 0 93 202 0 0 0 0.9019 142 129 74 48
uc.38 n 224 chr1:161127332-161127555 614407 CDCA1 \N PBX1 588881 0 0 0 0 0 0 0 0 0 224 0.0202 224 195 0 0
uc.39 n 356 chr1:161210912-161211267 697987 CDCA1 \N PBX1 505169 0 0 0 0 0 0 0 0 0 356 0.3389 356 338 262 208
uc.40 p 247 chr1:161825339-161825585 1312414 CDCA1 PBX1 LMX1A 534716 0 0 0 134 0 0 247 0 0 0 0.0252 141 132 0 0
uc.41 n 216 chr1:210655265-210655480 151959 RPS6KC1 \N PROX1 562303 0 0 0 0 0 0 0 0 0 216 0.0124 216 212 194 137
uc.42 n 266 chr1:212945530-212945795 93884 AF155110 \N USH2A 457996 0 0 0 0 0 0 0 0 0 266 0.0594 266 265 197 167
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.43 n 257 chr1:240842759-240843015 232641 SDCCAG8 AKT3 ZNF238 320290 0 0 0 0 0 0 257 0 0 0 0.1236 257 251 0 0
uc.44 e 230 chr1:241164431-241164660 211234 AKT3 ZNF238 AK124614 9695 230 191 230 230 0 230 0 0 0 0 0.0586 230 218 230 144
uc.45 e 203 chr1:241963410-241963612 9728 LOC116228 HNRPU AK095945 115772 203 0 203 203 198 0 0 5 5 0 0.1298 203 186 0 0
uc.46 e 217 chr1:241964327-241964543 10645 LOC116228 HNRPU AK095945 114841 203 203 203 217 149 54 14 0 0 0 0.6011 210 204 217 128
uc.47 n 227 chr2:7796390-7796616 590426 RNF144 \N AK125905 212606 0 0 0 0 0 0 0 0 0 227 0.0531 227 226 167 123
uc.48 e 298 chr2:20462845-20463142 53461 SDC1 PUM2 ARHB 168596 237 237 244 258 0 237 298 0 0 0 0.3291 292 285 292 181
uc.49 e 207 chr2:33787944-33788150 23748 RASGRP3 AK074867 AK057470 137707 207 178 207 181 0 178 29 0 0 0 0.8197 207 179 207 144
uc.50 e 222 chr2:38950836-38951057 14775 GALM SFRS7 GEMIN6 28836 222 222 222 222 160 28 222 0 0 0 0.4063 222 212 0 0
uc.51 n 207 chr2:57947093-57947299 1359250 AB067499 \N VRK2 301060 0 0 0 0 0 0 0 0 0 207 0.2689 207 207 0 0
uc.52 n 274 chr2:59082720-59082993 639695 FANCL \N BCL11A 1569842 0 0 0 0 0 0 0 0 0 274 0.0871 274 270 0 0
uc.53 n 232 chr2:59107845-59108076 664820 FANCL \N BCL11A 1544759 0 0 0 0 0 0 0 0 0 232 0.1151 232 225 0 0
uc.54 n 209 chr2:59173937-59174145 730912 FANCL \N BCL11A 1478690 0 0 0 0 0 0 0 0 0 209 0.014 209 206 0 0
uc.55 n 240 chr2:59721112-59721351 1278087 FANCL \N BCL11A 931484 0 0 0 0 0 0 0 0 0 240 0.1186 240 227 0 0
uc.56 n 202 chr2:59922365-59922566 1479340 FANCL \N BCL11A 730269 0 0 0 0 0 0 0 0 0 202 0.2733 202 201 0 0
uc.57 n 246 chr2:60113774-60114019 1670749 FANCL \N BCL11A 538816 0 0 0 0 0 0 0 0 0 246 0.0294 0 0 184 138
uc.58 n 203 chr2:60272497-60272699 1829472 FANCL \N BCL11A 380136 0 0 0 0 0 0 0 0 0 203 0.4592 203 203 203 184
uc.59 n 220 chr2:60272917-60273136 1829892 FANCL \N BCL11A 379699 0 0 0 0 0 0 0 0 0 220 0.4273 220 211 178 104
uc.60 n 217 chr2:60416094-60416310 1973069 FANCL \N BCL11A 236525 0 0 0 0 0 0 0 0 0 217 0.0137 137 119 133 118
uc.61 e 326 chr2:60662107-60662432 2219082 FANCL BCL11A PAPOLG 295706 326 82 326 326 0 326 326 0 0 0 0.0181 326 304 326 250
uc.62 e 234 chr2:60755216-60755449 2312191 FANCL BCL11A PAPOLG 202689 87 5 87 222 87 0 0 147 0 0 0.0508 37 26 222 152
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.63 e 278 chr2:61727035-61727312 54511 USP34 XPO1 AK023367 310413 152 0 152 276 0 0 278 0 0 0 0.0195 278 266 117 69
uc.64 p 245 chr2:63168625-63168869 460614 TMEM17 NACSIN OTX1 83657 0 0 245 245 0 0 245 0 0 0 0.2002 245 244 210 136
uc.65 n 212 chr2:66273125-66273336 639280 SPRED2 \N MEIS1 363729 0 0 0 0 0 0 0 0 0 212 0.0783 212 201 0 0
uc.66 n 247 chr2:73149541-73149787 13526 EMX1 SFXN5 GAF1 125259 0 0 0 0 0 0 247 0 0 0 0.0707 247 229 0 0
uc.67 n 217 chr2:104358126-104358342 1302855 FLJ30294 \N POU3F3 735026 0 0 0 0 0 0 0 0 0 217 0.1225 217 215 119 89
uc.68 n 255 chr2:144125491-144125745 114847 KYNU ARHGAP15 AK126774 782131 0 0 0 0 0 0 255 0 0 0 0.4332 255 255 221 169
uc.69 n 301 chr2:144322879-144323179 312235 KYNU ARHGAP15 AK126774 584697 0 0 0 0 0 0 301 0 0 0 0.1277 145 145 0 0
uc.70 p 237 chr2:144648108-144648344 637464 KYNU ARHGAP15 AK126774 259532 0 0 0 237 0 0 237 0 0 0 0.0567 237 234 237 181
uc.71 n 248 chr2:144923625-144923872 12536 AK126774 BC017741 ZFHX1B 432481 0 0 0 0 0 0 248 0 0 0 0.2838 248 242 129 83
uc.72 n 407 chr2:144925741-144926147 14652 AK126774 BC017741 ZFHX1B 430206 0 0 0 0 0 0 407 0 0 0 0.1375 407 407 407 350
uc.73 p 201 chr2:144973082-144973282 61993 AK126774 BC017741 ZFHX1B 383071 0 0 0 181 0 0 201 0 0 0 0.2973 178 175 177 124
uc.74 p 538 chr2:145036732-145037269 125643 AK126774 BC017741 ZFHX1B 319084 0 0 537 0 0 0 538 0 0 0 0.1131 538 537 217 194
uc.75 e 236 chr2:145356619-145356854 55811 BC017741 ZFHX1B AK098835 72593 236 0 236 236 236 0 0 0 0 0 0.319 228 228 224 194
uc.76 n 335 chr2:145371902-145372236 71094 BC017741 ZFHX1B AK098835 57211 0 0 0 7 0 0 335 0 0 0 0.5486 335 330 216 172
uc.77 e 296 chr2:145396534-145396829 95726 BC017741 ZFHX1B AK098835 32618 296 0 296 296 296 0 296 0 0 0 0.4681 296 294 262 226
uc.78 n 248 chr2:145399123-145399370 98315 BC017741 ZFHX1B AK098835 30077 0 0 0 0 0 0 248 0 0 0 0.4486 248 236 110 83
uc.79 p 295 chr2:145407946-145408240 107138 BC017741 ZFHX1B AK098835 21207 0 0 0 21 0 0 295 0 0 0 0.3429 295 293 0 0
uc.80 n 294 chr2:145411621-145411914 110813 BC017741 ZFHX1B AK098835 17533 0 0 0 0 0 0 294 0 0 0 0.0151 294 291 0 0
uc.81 n 211 chr2:147344834-147345044 1856184 ZFHX1B \N ACVR2 1467909 0 0 0 0 0 0 0 0 0 211 0.0947 211 209 211 159
uc.82 n 210 chr2:156929644-156929853 78091 AK096400 \N NR4A2 453642 0 0 0 0 0 0 0 0 0 210 0.192 210 208 177 122
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.83 n 296 chr2:157194172-157194467 342619 AK096400 \N NR4A2 189028 0 0 0 0 0 0 0 0 0 296 0.0062 296 295 296 275
uc.84 p 209 chr2:157397251-157397459 5522 NR4A2 \N GPD2 97307 209 0 209 202 0 0 0 209 0 0 0.0991 209 199 0 0
uc.85 n 248 chr2:157753959-157754206 111497 GPD2 \N GALNT5 562678 0 0 0 0 0 0 0 0 0 248 0.1195 248 247 248 230
uc.86 n 340 chr2:157862655-157862994 220193 GPD2 \N GALNT5 453890 0 0 0 0 0 0 0 0 0 340 0.4349 340 338 0 0
uc.87 n 290 chr2:158102814-158103103 460352 GPD2 \N GALNT5 213781 0 0 0 0 0 0 0 0 0 290 0.6705 290 281 276 174
uc.88 n 312 chr2:162297586-162297897 2359 TANK \N PSMD14 69700 0 0 0 0 0 0 0 0 312 0 0.0095 272 260 272 219
uc.89 p 307 chr2:162441217-162441523 145990 TANK PSMD14 TBR1 33918 0 0 0 295 0 0 307 0 0 0 0.1304 307 303 0 0
uc.90 e 206 chr2:162475571-162475776 4800 PSMD14 TBR1 AK095511 17152 206 206 206 206 0 206 0 0 0 0 0.1748 206 199 206 168
uc.91 n 207 chr2:163247566-163247772 36264 GCG FAP MDA5 78361 0 0 7 0 0 0 207 0 0 0 0.5494 0 0 25 14
uc.92 n 309 chr2:164653223-164653531 755438 KCNH7 \N FIGN 13137 0 0 0 0 0 0 0 0 0 309 0.0809 309 308 309 269
uc.93 n 263 chr2:164864451-164864713 193762 FIGN \N GRB14 687163 0 0 0 0 0 0 0 0 0 263 0.0007 263 262 249 194
uc.94 n 200 chr2:165046714-165046913 376025 FIGN \N GRB14 504963 0 0 0 0 0 0 0 0 0 200 0.0207 200 199 194 142
uc.95 p 251 chr2:171774074-171774324 452 AK123485 \N GAD1 101291 0 0 244 251 0 0 0 251 0 0 0.1473 251 243 251 235
uc.96 p 261 chr2:173023218-173023478 69928 SLC25A12 HAT1 DLX1 129306 0 0 0 145 0 0 261 0 0 0 0.0539 261 250 0 0
uc.97 e 442 chr2:173025175-173025616 71885 SLC25A12 HAT1 DLX1 127168 442 112 442 116 0 105 337 0 0 0 0.2843 442 432 442 331
uc.98 n 238 chr2:173159062-173159299 2118 DLX1 \N DLX2 7705 0 0 0 0 0 0 0 0 238 0 0.1343 238 236 237 179
uc.99 n 398 chr2:173160925-173161322 3981 DLX1 \N DLX2 5682 0 0 0 0 0 0 0 0 398 0 0.065 398 395 398 348
uc.100 n 207 chr2:174317324-174317530 197164 RAPGEF4 ZAK CDCA7 104593 0 0 0 0 0 0 207 0 0 0 0.0282 207 207 92 83
uc.101 e 254 chr2:174977025-174977278 204375 M19503 SP3 AK095037 77599 254 254 254 254 188 66 0 0 0 0 0.3511 254 246 233 142
uc.102 e 338 chr2:175148953-175149290 91488 AK095037 PTD004 AK128215 252419 95 97 95 226 0 95 243 0 0 0 0.1274 338 332 335 249
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.103 p 233 chr2:175172216-175172448 114751 AK095037 PTD004 AK128215 229261 0 0 0 233 0 0 233 0 0 0 0.1949 233 220 196 166
uc.104 n 216 chr2:175189478-175189693 132013 AK095037 PTD004 AK128215 212016 0 0 0 0 0 0 216 0 0 0 0.2721 216 210 216 132
uc.105 n 223 chr2:175192331-175192553 134866 AK095037 PTD004 AK128215 209156 0 0 0 0 0 0 223 0 0 0 0.0371 223 221 167 122
uc.106 p 206 chr2:175227967-175228172 170502 AK095037 PTD004 AK128215 173537 0 0 0 37 0 0 206 0 0 0 0.7216 206 199 0 0
uc.107 n 237 chr2:175410152-175410388 5313 AK128215 \N CIR 5035 0 0 0 0 0 0 0 237 237 0 0.0299 154 142 0 0
uc.108 n 374 chr2:177142901-177143274 73365 KIAA1715 \N HOXD13 16801 0 0 0 0 0 0 0 0 0 374 0.1367 314 310 374 355
uc.109 n 224 chr2:177705882-177706105 678 BC013438 \N hnRNPA3 573966 0 0 0 0 0 0 0 224 0 0 0.2664 224 222 0 0
uc.110 n 243 chr2:237358132-237358374 37490 CENTG2 \N GBX2 2843 0 0 0 0 0 0 0 0 243 0 0.3266 243 228 32 18
uc.111 p 296 chr3:9446461-9446756 32708 AK128398 \N AB051544 3920 225 225 246 296 0 0 0 296 0 0 0.0018 0 0 0 0
uc.483 p 402 chr3:17567733-17568134 351576 AK125129 TBC1D5 SATB1 797109 0 0 0 41 0 0 402 0 0 0 0.0344 402 400 402 334
uc.112 n 346 chr3:18144568-18144913 387164 TBC1D5 \N SATB1 220330 0 0 0 0 0 0 0 0 0 346 0.1555 338 337 338 299
uc.113 p 247 chr3:18651408-18651654 196199 SATB1 \N KCNH8 513366 0 0 0 22 0 0 0 0 0 247 0.0782 247 215 0 0
uc.114 n 294 chr3:18819454-18819747 364245 SATB1 \N KCNH8 345273 0 0 0 0 0 0 0 0 0 294 0.1157 294 280 291 195
uc.115 n 219 chr3:19009162-19009380 553953 SATB1 \N KCNH8 155640 0 0 0 0 0 0 0 0 0 219 0.2977 219 215 0 0
uc.116 n 206 chr3:70499494-70499699 548937 MITF \N AK125942 96119 0 0 0 0 0 0 0 0 0 206 0.0018 206 200 206 152
uc.117 n 251 chr3:70792683-70792933 192800 AK125942 \N FOXP1 136271 0 0 0 0 0 0 0 0 0 251 0.4338 251 245 251 218
uc.118 n 219 chr3:70792935-70793153 193052 AK125942 \N FOXP1 136051 0 0 0 0 0 0 0 0 0 219 0.1466 219 217 74 41
uc.119 n 301 chr3:115754368-115754668 40423 AF116655 ZNF288 AF119886 405251 0 0 0 0 0 0 301 0 0 0 0.2937 300 292 0 0
uc.120 p 270 chr3:115755940-115756209 41995 AF116655 ZNF288 AF119886 403710 0 0 0 263 0 0 270 0 0 0 0.0063 270 260 0 0
uc.121 n 293 chr3:115896375-115896667 97686 ZNF288 \N AF119886 263252 0 0 0 0 0 0 0 0 0 293 0.3077 293 288 0 0
ultra conserved element upstream gene within downstream gene Human Any Species Known Gene Overlap RNAfold chicken Fugu
name type length Build 34 (hg16) coords distance name gene name distance mRNA spliced EST mRNA EST UTR CDS intron 10k upstr 10k down intergenic p-value overlap identical overlap identical
uc.122 n 215 chr3:115932792-115933006 134103 ZNF288 \N AF119886 226913 0 0 0 0 0 0 0 0 0 215 0.1466 215 203 0 0
uc.123 n 492 chr3:138304453-138304944 253619 MGC34923 \N SOX14 499543 0 0 0 0 0 0 0 0 0 492 0.0814 492 482 483 432
uc.124 n 287 chr3:138369353-138369639 318519 MGC34923 \N SOX14 434848 0 0 0 9 0 0 0 0 0 287 0.064 287 284 266 243
uc.125 n 265 chr3:138389226-138389490 338392 MGC34923 \N SOX14 414997 0 0 0 0 0 0 0 0 0 265 0.0714 265 261 243 156
uc.126 n 271 chr3:138446557-138446827 395723 MGC34923 \N SOX14 357660 0 0 0 0 0 0 0 0 0 271 0.027 271 271 257 237
uc.127 n 272 chr3:148351617-148351888 768212 PLSCR1 \N ZIC4 74353 0 0 0 0 0 0 0 0 0 272 0.4969 272 267 272 222
uc.128 p 299 chr3:148370547-148370845 787142 PLSCR1 \N ZIC4 55396 0 0 0 201 0 0 0 0 0 299 0.0517 299 295 299 238
uc.129 e 212 chr3:153485296-153485507 105607 AY358260 MBNL1 P2RY1 388137 54 55 55 166 0 54 212 0 0 0 0.6306 212 181 212 204
uc.130 p 224 chr3:159097487-159097710 457554 BC029129 \N SHOX2 37047 0 0 0 224 0 0 0 0 0 224 0.0406 224 220 224 202
uc.131 n 207 chr3:159310953-159311159 156935 AF257098 MGC12197 MLF1 298736 0 0 0 0 0 0 207 0 0 0 0.2111 207 203 207 160
uc.132 n 208 chr3:159347072-159347279 193054 AF257098 MGC12197 MLF1 262616 0 0 0 0 0 0 208 0 0 0 0.0442 208 203 208 122
uc.133 n 277 chr3:159347391-159347667 193373 AF257098 MGC12197 MLF1 262228 0 0 0 0 0 0 277 0 0 0 0.2992 277 275 221 202
uc.134 p 211 chr3:159566817-159567027 412799 AF257098 MGC12197 MLF1 42868 0 0 211 211 0 0 211 0 0 0 0.0323 211 203 211 193
uc.135 e 201 chr3:170155196-170155396 1021196 GOLPH4 EVI1 ARPM1 650229 201 201 201 201 0 201 201 0 0 0 0.2597 201 198 201 137
uc.136 p 347 chr3:170514865-170515211 94639 EVI1 AK096400 ARPM1 290414 0 0 0 230 0 0 347 0 0 0 0.3433 347 341 0 0
uc.137 n 385 chr3:181757770-181758154 101240 TTC14 AL122120 FXR1 193220 0 0 0 0 0 0 385 0 0 0 0.1278 385 382 0 0
uc.138 e 419 chr3:186970209-186970627 106483 IMP-2 SFRS10 ETV5 115887 93 277 345 419 0 0 419 0 0 0 0.4022 419 407 347 206
uc.139 p 338 chr4:4587982-4588319 102655 D4S234E STX18 MSX1 337647 0 0 0 224 0 0 338 0 0 0 0.8228 338 315 338 213
uc.140 n 223 chr4:12760753-12760975 1579350 HS3ST1 \N BC035054 359255 0 0 0 0 0 0 0 0 0 223 0.4441 223 210 0 0
uc.141 e 295</

ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.1	p	207	chr1:10307243-10307449	65151	DFFA	PEX14	AK130996	99286	0	0	0	66	0	0	207	0	0	0	0.0988	207	196	0	0
uc.2	n	207	chr1:10442089-10442295	34690	AK130996	FLJ20321	FLJ37118	273783	0	0	0	0	0	0	207	0	0	0	0.8707	189	189	0	0
uc.3	p	225	chr1:10460711-10460935	53312	AK130996	FLJ20321	FLJ37118	255143	0	0	0	222	0	0	225	0	0	0	0.1818	225	212	0	0
uc.4	n	359	chr1:10467795-10468153	4286	FLJ20321	\N	FLJ37118	247925	0	0	0	0	0	0	0	359	0	0	0.4531	359	347	359	287
uc.5	n	214	chr1:10490897-10491110	27388	FLJ20321	\N	FLJ37118	224968	0	0	0	0	0	0	0	0	0	214	0.0574	213	212	200	179
uc.6	p	301	chr1:10504667-10504967	41158	FLJ20321	\N	FLJ37118	211111	0	0	0	301	0	0	0	0	0	301	0.2363	301	288	279	237
uc.7	p	256	chr1:10545679-10545934	82170	FLJ20321	\N	FLJ37118	170144	0	0	0	235	0	0	0	0	0	256	0.2663	256	247	0	0
uc.8	n	216	chr1:10561364-10561579	97855	FLJ20321	\N	FLJ37118	154499	0	0	0	0	0	0	0	0	0	216	0.2285	207	202	207	172
uc.9	n	202	chr1:10634956-10635157	171447	FLJ20321	\N	FLJ37118	80921	0	0	0	0	0	0	0	0	0	202	0.0222	202	195	0	0
uc.10	n	275	chr1:10675120-10675394	211611	FLJ20321	\N	FLJ37118	40684	0	0	0	0	0	0	0	0	0	275	0.0177	275	273	275	250
uc.12	p	201	chr1:35077889-35078089	68766	FLJ23151	SFPQ	ZNF262	140539	0	0	0	201	0	0	201	0	0	0	0.6008	201	189	201	110
uc.13	e	237	chr1:35786852-35787088	36769	EIF2C4	EIF2C1	EIF2C3	36892	137	137	197	199	0	137	100	0	0	0	0.1805	201	162	160	134
uc.14	p	213	chr1:37908298-37908510	5531	CGI-94	\N	POU3F1	15061	0	0	0	10	0	0	0	0	213	0	0.3971	213	185	0	0
uc.15	n	233	chr1:37974370-37974602	48625	POU3F1	\N	RRAGC	742565	0	0	0	0	0	0	0	0	0	233	0.4661	233	229	197	183
uc.16	p	211	chr1:38041493-38041703	115748	POU3F1	\N	RRAGC	675464	0	0	0	24	0	0	0	0	0	211	0.0929	211	180	0	0
uc.17	n	237	chr1:38215445-38215681	289700	POU3F1	\N	RRAGC	501486	0	0	0	0	0	0	0	0	0	237	0.3543	237	171	0	0
uc.18	n	238	chr1:44128955-44129192	29316	DMAP1	PRNPIP	FLJ10597	382114	0	0	0	0	0	0	238	0	0	0	0.214	224	209	0	0
uc.19	n	256	chr1:44403606-44403861	169431	PRNPIP	\N	FLJ10597	107445	0	0	0	0	0	0	0	0	0	256	0.8574	256	244	0	0
uc.20	p	269	chr1:44415666-44415934	181491	PRNPIP	\N	FLJ10597	95372	0	0	0	25	0	0	0	0	0	269	0.7435	269	239	0	0
uc.21	n	235	chr1:48482903-48483137	175140	SPATA6	FLJ14442	FLJ11588	80321	0	0	0	0	0	0	235	0	0	0	0.1828	235	223	0	0
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.22	n	308	chr1:50376149-50376456	119188	DMRTA2	FAF1	LOC51336	413691	0	0	0	0	0	0	308	0	0	0	0.1317	308	300	284	179
uc.23	n	229	chr1:50405695-50405923	148734	DMRTA2	FAF1	LOC51336	384224	0	0	0	0	0	0	229	0	0	0	0.025	229	226	152	112
uc.24	n	336	chr1:50469063-50469398	212102	DMRTA2	FAF1	LOC51336	320749	0	0	0	0	0	0	336	0	0	0	0.2441	336	331	0	0
uc.25	n	235	chr1:50535952-50536186	278991	DMRTA2	FAF1	LOC51336	253961	0	0	0	0	0	0	235	0	0	0	0.162	235	233	77	54
uc.26	n	212	chr1:62739563-62739774	38822	AUTL1	\N	FOXD3	419268	0	0	0	0	0	0	0	0	0	212	0.2032	212	212	212	191
uc.27	n	290	chr1:62739797-62740086	39056	AUTL1	\N	FOXD3	418956	0	0	0	0	0	0	0	0	0	290	0.0501	290	290	290	273
uc.28	e	355	chr1:70066629-70066983	25453	FLJ20331	SFRS11	DKFZP566D1346	29852	355	181	355	355	355	0	355	0	0	0	0.0883	355	340	167	132
uc.29	n	219	chr1:87244976-87245194	11120	LMO4	\N	AF118089	1371952	0	0	0	0	0	0	0	0	0	219	0.0045	219	219	219	209
uc.30	n	243	chr1:87451593-87451835	217737	LMO4	\N	AF118089	1165311	0	0	0	0	0	0	0	0	0	243	0.2468	243	239	0	0
uc.31	n	253	chr1:88395168-88395420	1161312	LMO4	\N	AF118089	221726	0	0	0	0	0	0	0	0	0	253	0.0118	168	165	103	92
uc.33	e	312	chr1:96743538-96743849	9890	BC030757	PTBP2	DPYD	271253	34	36	34	269	0	34	312	0	0	0	0.3978	252	251	201	124
uc.34	e	208	chr1:96751973-96752180	18325	BC030757	PTBP2	DPYD	262922	176	0	208	208	176	0	0	0	32	0	0.0164	208	204	62	31
uc.35	p	205	chr1:97465205-97465409	713056	PTBP2	DPYD	AK092728	506426	0	0	0	165	0	0	205	0	0	0	0.2712	205	186	0	0
uc.36	p	264	chr1:108587040-108587303	36279	FLJ30525	FLJ10330	FLJ35838	24296	0	0	158	264	0	0	264	0	0	0	0.1423	264	258	0	0
uc.37	e	202	chr1:114578780-114578981	41876	AMPD1	D1S155E	FLJ21168	35142	93	102	202	202	0	93	202	0	0	0	0.9019	142	129	74	48
uc.38	n	224	chr1:161127332-161127555	614407	CDCA1	\N	PBX1	588881	0	0	0	0	0	0	0	0	0	224	0.0202	224	195	0	0
uc.39	n	356	chr1:161210912-161211267	697987	CDCA1	\N	PBX1	505169	0	0	0	0	0	0	0	0	0	356	0.3389	356	338	262	208
uc.40	p	247	chr1:161825339-161825585	1312414	CDCA1	PBX1	LMX1A	534716	0	0	0	134	0	0	247	0	0	0	0.0252	141	132	0	0
uc.41	n	216	chr1:210655265-210655480	151959	RPS6KC1	\N	PROX1	562303	0	0	0	0	0	0	0	0	0	216	0.0124	216	212	194	137
uc.42	n	266	chr1:212945530-212945795	93884	AF155110	\N	USH2A	457996	0	0	0	0	0	0	0	0	0	266	0.0594	266	265	197	167
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.43	n	257	chr1:240842759-240843015	232641	SDCCAG8	AKT3	ZNF238	320290	0	0	0	0	0	0	257	0	0	0	0.1236	257	251	0	0
uc.44	e	230	chr1:241164431-241164660	211234	AKT3	ZNF238	AK124614	9695	230	191	230	230	0	230	0	0	0	0	0.0586	230	218	230	144
uc.45	e	203	chr1:241963410-241963612	9728	LOC116228	HNRPU	AK095945	115772	203	0	203	203	198	0	0	5	5	0	0.1298	203	186	0	0
uc.46	e	217	chr1:241964327-241964543	10645	LOC116228	HNRPU	AK095945	114841	203	203	203	217	149	54	14	0	0	0	0.6011	210	204	217	128
uc.47	n	227	chr2:7796390-7796616	590426	RNF144	\N	AK125905	212606	0	0	0	0	0	0	0	0	0	227	0.0531	227	226	167	123
uc.48	e	298	chr2:20462845-20463142	53461	SDC1	PUM2	ARHB	168596	237	237	244	258	0	237	298	0	0	0	0.3291	292	285	292	181
uc.49	e	207	chr2:33787944-33788150	23748	RASGRP3	AK074867	AK057470	137707	207	178	207	181	0	178	29	0	0	0	0.8197	207	179	207	144
uc.50	e	222	chr2:38950836-38951057	14775	GALM	SFRS7	GEMIN6	28836	222	222	222	222	160	28	222	0	0	0	0.4063	222	212	0	0
uc.51	n	207	chr2:57947093-57947299	1359250	AB067499	\N	VRK2	301060	0	0	0	0	0	0	0	0	0	207	0.2689	207	207	0	0
uc.52	n	274	chr2:59082720-59082993	639695	FANCL	\N	BCL11A	1569842	0	0	0	0	0	0	0	0	0	274	0.0871	274	270	0	0
uc.53	n	232	chr2:59107845-59108076	664820	FANCL	\N	BCL11A	1544759	0	0	0	0	0	0	0	0	0	232	0.1151	232	225	0	0
uc.54	n	209	chr2:59173937-59174145	730912	FANCL	\N	BCL11A	1478690	0	0	0	0	0	0	0	0	0	209	0.014	209	206	0	0
uc.55	n	240	chr2:59721112-59721351	1278087	FANCL	\N	BCL11A	931484	0	0	0	0	0	0	0	0	0	240	0.1186	240	227	0	0
uc.56	n	202	chr2:59922365-59922566	1479340	FANCL	\N	BCL11A	730269	0	0	0	0	0	0	0	0	0	202	0.2733	202	201	0	0
uc.57	n	246	chr2:60113774-60114019	1670749	FANCL	\N	BCL11A	538816	0	0	0	0	0	0	0	0	0	246	0.0294	0	0	184	138
uc.58	n	203	chr2:60272497-60272699	1829472	FANCL	\N	BCL11A	380136	0	0	0	0	0	0	0	0	0	203	0.4592	203	203	203	184
uc.59	n	220	chr2:60272917-60273136	1829892	FANCL	\N	BCL11A	379699	0	0	0	0	0	0	0	0	0	220	0.4273	220	211	178	104
uc.60	n	217	chr2:60416094-60416310	1973069	FANCL	\N	BCL11A	236525	0	0	0	0	0	0	0	0	0	217	0.0137	137	119	133	118
uc.61	e	326	chr2:60662107-60662432	2219082	FANCL	BCL11A	PAPOLG	295706	326	82	326	326	0	326	326	0	0	0	0.0181	326	304	326	250
uc.62	e	234	chr2:60755216-60755449	2312191	FANCL	BCL11A	PAPOLG	202689	87	5	87	222	87	0	0	147	0	0	0.0508	37	26	222	152
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.63	e	278	chr2:61727035-61727312	54511	USP34	XPO1	AK023367	310413	152	0	152	276	0	0	278	0	0	0	0.0195	278	266	117	69
uc.64	p	245	chr2:63168625-63168869	460614	TMEM17	NACSIN	OTX1	83657	0	0	245	245	0	0	245	0	0	0	0.2002	245	244	210	136
uc.65	n	212	chr2:66273125-66273336	639280	SPRED2	\N	MEIS1	363729	0	0	0	0	0	0	0	0	0	212	0.0783	212	201	0	0
uc.66	n	247	chr2:73149541-73149787	13526	EMX1	SFXN5	GAF1	125259	0	0	0	0	0	0	247	0	0	0	0.0707	247	229	0	0
uc.67	n	217	chr2:104358126-104358342	1302855	FLJ30294	\N	POU3F3	735026	0	0	0	0	0	0	0	0	0	217	0.1225	217	215	119	89
uc.68	n	255	chr2:144125491-144125745	114847	KYNU	ARHGAP15	AK126774	782131	0	0	0	0	0	0	255	0	0	0	0.4332	255	255	221	169
uc.69	n	301	chr2:144322879-144323179	312235	KYNU	ARHGAP15	AK126774	584697	0	0	0	0	0	0	301	0	0	0	0.1277	145	145	0	0
uc.70	p	237	chr2:144648108-144648344	637464	KYNU	ARHGAP15	AK126774	259532	0	0	0	237	0	0	237	0	0	0	0.0567	237	234	237	181
uc.71	n	248	chr2:144923625-144923872	12536	AK126774	BC017741	ZFHX1B	432481	0	0	0	0	0	0	248	0	0	0	0.2838	248	242	129	83
uc.72	n	407	chr2:144925741-144926147	14652	AK126774	BC017741	ZFHX1B	430206	0	0	0	0	0	0	407	0	0	0	0.1375	407	407	407	350
uc.73	p	201	chr2:144973082-144973282	61993	AK126774	BC017741	ZFHX1B	383071	0	0	0	181	0	0	201	0	0	0	0.2973	178	175	177	124
uc.74	p	538	chr2:145036732-145037269	125643	AK126774	BC017741	ZFHX1B	319084	0	0	537	0	0	0	538	0	0	0	0.1131	538	537	217	194
uc.75	e	236	chr2:145356619-145356854	55811	BC017741	ZFHX1B	AK098835	72593	236	0	236	236	236	0	0	0	0	0	0.319	228	228	224	194
uc.76	n	335	chr2:145371902-145372236	71094	BC017741	ZFHX1B	AK098835	57211	0	0	0	7	0	0	335	0	0	0	0.5486	335	330	216	172
uc.77	e	296	chr2:145396534-145396829	95726	BC017741	ZFHX1B	AK098835	32618	296	0	296	296	296	0	296	0	0	0	0.4681	296	294	262	226
uc.78	n	248	chr2:145399123-145399370	98315	BC017741	ZFHX1B	AK098835	30077	0	0	0	0	0	0	248	0	0	0	0.4486	248	236	110	83
uc.79	p	295	chr2:145407946-145408240	107138	BC017741	ZFHX1B	AK098835	21207	0	0	0	21	0	0	295	0	0	0	0.3429	295	293	0	0
uc.80	n	294	chr2:145411621-145411914	110813	BC017741	ZFHX1B	AK098835	17533	0	0	0	0	0	0	294	0	0	0	0.0151	294	291	0	0
uc.81	n	211	chr2:147344834-147345044	1856184	ZFHX1B	\N	ACVR2	1467909	0	0	0	0	0	0	0	0	0	211	0.0947	211	209	211	159
uc.82	n	210	chr2:156929644-156929853	78091	AK096400	\N	NR4A2	453642	0	0	0	0	0	0	0	0	0	210	0.192	210	208	177	122
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.83	n	296	chr2:157194172-157194467	342619	AK096400	\N	NR4A2	189028	0	0	0	0	0	0	0	0	0	296	0.0062	296	295	296	275
uc.84	p	209	chr2:157397251-157397459	5522	NR4A2	\N	GPD2	97307	209	0	209	202	0	0	0	209	0	0	0.0991	209	199	0	0
uc.85	n	248	chr2:157753959-157754206	111497	GPD2	\N	GALNT5	562678	0	0	0	0	0	0	0	0	0	248	0.1195	248	247	248	230
uc.86	n	340	chr2:157862655-157862994	220193	GPD2	\N	GALNT5	453890	0	0	0	0	0	0	0	0	0	340	0.4349	340	338	0	0
uc.87	n	290	chr2:158102814-158103103	460352	GPD2	\N	GALNT5	213781	0	0	0	0	0	0	0	0	0	290	0.6705	290	281	276	174
uc.88	n	312	chr2:162297586-162297897	2359	TANK	\N	PSMD14	69700	0	0	0	0	0	0	0	0	312	0	0.0095	272	260	272	219
uc.89	p	307	chr2:162441217-162441523	145990	TANK	PSMD14	TBR1	33918	0	0	0	295	0	0	307	0	0	0	0.1304	307	303	0	0
uc.90	e	206	chr2:162475571-162475776	4800	PSMD14	TBR1	AK095511	17152	206	206	206	206	0	206	0	0	0	0	0.1748	206	199	206	168
uc.91	n	207	chr2:163247566-163247772	36264	GCG	FAP	MDA5	78361	0	0	7	0	0	0	207	0	0	0	0.5494	0	0	25	14
uc.92	n	309	chr2:164653223-164653531	755438	KCNH7	\N	FIGN	13137	0	0	0	0	0	0	0	0	0	309	0.0809	309	308	309	269
uc.93	n	263	chr2:164864451-164864713	193762	FIGN	\N	GRB14	687163	0	0	0	0	0	0	0	0	0	263	0.0007	263	262	249	194
uc.94	n	200	chr2:165046714-165046913	376025	FIGN	\N	GRB14	504963	0	0	0	0	0	0	0	0	0	200	0.0207	200	199	194	142
uc.95	p	251	chr2:171774074-171774324	452	AK123485	\N	GAD1	101291	0	0	244	251	0	0	0	251	0	0	0.1473	251	243	251	235
uc.96	p	261	chr2:173023218-173023478	69928	SLC25A12	HAT1	DLX1	129306	0	0	0	145	0	0	261	0	0	0	0.0539	261	250	0	0
uc.97	e	442	chr2:173025175-173025616	71885	SLC25A12	HAT1	DLX1	127168	442	112	442	116	0	105	337	0	0	0	0.2843	442	432	442	331
uc.98	n	238	chr2:173159062-173159299	2118	DLX1	\N	DLX2	7705	0	0	0	0	0	0	0	0	238	0	0.1343	238	236	237	179
uc.99	n	398	chr2:173160925-173161322	3981	DLX1	\N	DLX2	5682	0	0	0	0	0	0	0	0	398	0	0.065	398	395	398	348
uc.100	n	207	chr2:174317324-174317530	197164	RAPGEF4	ZAK	CDCA7	104593	0	0	0	0	0	0	207	0	0	0	0.0282	207	207	92	83
uc.101	e	254	chr2:174977025-174977278	204375	M19503	SP3	AK095037	77599	254	254	254	254	188	66	0	0	0	0	0.3511	254	246	233	142
uc.102	e	338	chr2:175148953-175149290	91488	AK095037	PTD004	AK128215	252419	95	97	95	226	0	95	243	0	0	0	0.1274	338	332	335	249
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.103	p	233	chr2:175172216-175172448	114751	AK095037	PTD004	AK128215	229261	0	0	0	233	0	0	233	0	0	0	0.1949	233	220	196	166
uc.104	n	216	chr2:175189478-175189693	132013	AK095037	PTD004	AK128215	212016	0	0	0	0	0	0	216	0	0	0	0.2721	216	210	216	132
uc.105	n	223	chr2:175192331-175192553	134866	AK095037	PTD004	AK128215	209156	0	0	0	0	0	0	223	0	0	0	0.0371	223	221	167	122
uc.106	p	206	chr2:175227967-175228172	170502	AK095037	PTD004	AK128215	173537	0	0	0	37	0	0	206	0	0	0	0.7216	206	199	0	0
uc.107	n	237	chr2:175410152-175410388	5313	AK128215	\N	CIR	5035	0	0	0	0	0	0	0	237	237	0	0.0299	154	142	0	0
uc.108	n	374	chr2:177142901-177143274	73365	KIAA1715	\N	HOXD13	16801	0	0	0	0	0	0	0	0	0	374	0.1367	314	310	374	355
uc.109	n	224	chr2:177705882-177706105	678	BC013438	\N	hnRNPA3	573966	0	0	0	0	0	0	0	224	0	0	0.2664	224	222	0	0
uc.110	n	243	chr2:237358132-237358374	37490	CENTG2	\N	GBX2	2843	0	0	0	0	0	0	0	0	243	0	0.3266	243	228	32	18
uc.111	p	296	chr3:9446461-9446756	32708	AK128398	\N	AB051544	3920	225	225	246	296	0	0	0	296	0	0	0.0018	0	0	0	0
uc.483	p	402	chr3:17567733-17568134	351576	AK125129	TBC1D5	SATB1	797109	0	0	0	41	0	0	402	0	0	0	0.0344	402	400	402	334
uc.112	n	346	chr3:18144568-18144913	387164	TBC1D5	\N	SATB1	220330	0	0	0	0	0	0	0	0	0	346	0.1555	338	337	338	299
uc.113	p	247	chr3:18651408-18651654	196199	SATB1	\N	KCNH8	513366	0	0	0	22	0	0	0	0	0	247	0.0782	247	215	0	0
uc.114	n	294	chr3:18819454-18819747	364245	SATB1	\N	KCNH8	345273	0	0	0	0	0	0	0	0	0	294	0.1157	294	280	291	195
uc.115	n	219	chr3:19009162-19009380	553953	SATB1	\N	KCNH8	155640	0	0	0	0	0	0	0	0	0	219	0.2977	219	215	0	0
uc.116	n	206	chr3:70499494-70499699	548937	MITF	\N	AK125942	96119	0	0	0	0	0	0	0	0	0	206	0.0018	206	200	206	152
uc.117	n	251	chr3:70792683-70792933	192800	AK125942	\N	FOXP1	136271	0	0	0	0	0	0	0	0	0	251	0.4338	251	245	251	218
uc.118	n	219	chr3:70792935-70793153	193052	AK125942	\N	FOXP1	136051	0	0	0	0	0	0	0	0	0	219	0.1466	219	217	74	41
uc.119	n	301	chr3:115754368-115754668	40423	AF116655	ZNF288	AF119886	405251	0	0	0	0	0	0	301	0	0	0	0.2937	300	292	0	0
uc.120	p	270	chr3:115755940-115756209	41995	AF116655	ZNF288	AF119886	403710	0	0	0	263	0	0	270	0	0	0	0.0063	270	260	0	0
uc.121	n	293	chr3:115896375-115896667	97686	ZNF288	\N	AF119886	263252	0	0	0	0	0	0	0	0	0	293	0.3077	293	288	0	0
ultra conserved element				upstream gene		within	downstream gene		Human		Any Species		Known Gene Overlap						RNAfold	chicken		Fugu
name	type	length	Build 34 (hg16) coords	distance	name	gene	name	distance	mRNA	spliced EST	mRNA	EST	UTR	CDS	intron	10k upstr	10k down	intergenic	p-value	overlap	identical	overlap	identical
uc.122	n	215	chr3:115932792-115933006	134103	ZNF288	\N	AF119886	226913	0	0	0	0	0	0	0	0	0	215	0.1466	215	203	0	0
uc.123	n	492	chr3:138304453-138304944	253619	MGC34923	\N	SOX14	499543	0	0	0	0	0	0	0	0	0	492	0.0814	492	482	483	432
uc.124	n	287	chr3:138369353-138369639	318519	MGC34923	\N	SOX14	434848	0	0	0	9	0	0	0	0	0	287	0.064	287	284	266	243
uc.125	n	265	chr3:138389226-138389490	338392	MGC34923	\N	SOX14	414997	0	0	0	0	0	0	0	0	0	265	0.0714	265	261	243	156
uc.126	n	271	chr3:138446557-138446827	395723	MGC34923	\N	SOX14	357660	0	0	0	0	0	0	0	0	0	271	0.027	271	271	257	237
uc.127	n	272	chr3:148351617-148351888	768212	PLSCR1	\N	ZIC4	74353	0	0	0	0	0	0	0	0	0	272	0.4969	272	267	272	222
uc.128	p	299	chr3:148370547-148370845	787142	PLSCR1	\N	ZIC4	55396	0	0	0	201	0	0	0	0	0	299	0.0517	299	295	299	238
uc.129	e	212	chr3:153485296-153485507	105607	AY358260	MBNL1	P2RY1	388137	54	55	55	166	0	54	212	0	0	0	0.6306	212	181	212	204
uc.130	p	224	chr3:159097487-159097710	457554	BC029129	\N	SHOX2	37047	0	0	0	224	0	0	0	0	0	224	0.0406	224	220	224	202
uc.131	n	207	chr3:159310953-159311159	156935	AF257098	MGC12197	MLF1	298736	0	0	0	0	0	0	207	0	0	0	0.2111	207	203	207	160
uc.132	n	208	chr3:159347072-159347279	193054	AF257098	MGC12197	MLF1	262616	0	0	0	0	0	0	208	0	0	0	0.0442	208	203	208	122
uc.133	n	277	chr3:159347391-159347667	193373	AF257098	MGC12197	MLF1	262228	0	0	0	0	0	0	277	0	0	0	0.2992	277	275	221	202
uc.134	p	211	chr3:159566817-159567027	412799	AF257098	MGC12197	MLF1	42868	0	0	211	211	0	0	211	0	0	0	0.0323	211	203	211	193
uc.135	e	201	chr3:170155196-170155396	1021196	GOLPH4	EVI1	ARPM1	650229	201	201	201	201	0	201	201	0	0	0	0.2597	201	198	201	137
uc.136	p	347	chr3:170514865-170515211	94639	EVI1	AK096400	ARPM1	290414	0	0	0	230	0	0	347	0	0	0	0.3433	347	341	0	0
uc.137	n	385	chr3:181757770-181758154	101240	TTC14	AL122120	FXR1	193220	0	0	0	0	0	0	385	0	0	0	0.1278	385	382	0	0
uc.138	e	419	chr3:186970209-186970627	106483	IMP-2	SFRS10	ETV5	115887	93	277	345	419	0	0	419	0	0	0	0.4022	419	407	347	206
uc.139	p	338	chr4:4587982-4588319	102655	D4S234E	STX18	MSX1	337647	0	0	0	224	0	0	338	0	0	0	0.8228	338	315	338	213
uc.140	n	223	chr4:12760753-12760975	1579350	HS3ST1	\N	BC035054	359255	0	0	0	0	0	0	0	0	0	223	0.4441	223	210	0	0
uc.141	e	295</