Table 1. Identification of promoters of intergenic miRNA genes.
| miRNA | Chromosomal location | ChIP-chip region | CPPP Model | Predicted TSS (CPPP) | Distance |
| miR-200b∼miR-200a∼miR-429 | Chr1: 1092346 (+) | [1082033, 1083782] | CpG+ | 1083333 | 8763 |
| miR-34a | Chr1: 9134423 (−) | [9162283, 9166532] | CpG+ | 9163733 | 29310 |
| miR-101-1 | Chr1: 65296779 (−) | [65304283, 65307532] | CpG+ | 65305833 | 9054 |
| miR-181a-1∼miR-181b-1 | Chr1: 197094905 (−) | [197125783, 197127032] | CpG− | none predicted | NA |
| miR-202 | Chr10: 134911115 (−) | [134919994, 134925743] | CpG+ | 134924844 | 8879 |
| miR-210 | Chr11: 558198 (−) | [559355, 560354] | CpG+ | none predicted | NA |
| miR-194-2∼miR-192 | Chr11: 64415487 (−) | [64416605, 64418104] | CpG− | 64416930 | 1193 |
| miR-200c∼miR-141 | Chr12: 6943122 (+) | [6940546, 6942545] | CpG+ | 6941146 | 1976 |
| let-7i | Chr12: 61283732 (+) | [61279796, 61291045] | CpG+ | 61283796 | 506 |
| miR-379∼miR411∼…∼miR-410∼miR-656 | Chr14: 100558155 (+) | [100524119, 100525868] | CpG− | none predicted | NA |
| miR-193b | Chr16: 14305324 (+) | [14302031, 14310280] | CpG+ | 14304581 | 743 |
| miR-138-2 | Chr16: 55449930 (+) | [55439531, 55441030] | CpG− | 55439856 | 9824 |
| miR-497∼miR-195 | Chr17: 6862065 (−) | [6863309, 6865058] | CpG− | 6864759 | 2444 |
| miR-10a | Chr17: 44012308 (−) | [44017059, 44018808] | CpG+ | 44017709 | 5401 |
| miR-196a-1 | Chr17: 44064920 (−) | [44078809, 44080558] | CpG+ | 44079509 | 14589 |
| miR-21 | Chr17: 55273408 (+) | [55267309, 55276558] | CpG− | 55271984 | 1174 |
| miR-122 | Chr18: 54269285 (+) | [54235566, 54236565] | CpG− | 54235891 | 33144 |
| miR-23a∼miR-27a∼miR-24-2 | Chr19: 13808473 (−) | [13807348, 13809097] | CpG− | 13808448 | 0 |
| miR-181c∼miR-181d | Chr19: 13846512 (+) | [13832848, 13834847] | CpG− | none predicted | NA |
| miR-99b∼let-7e∼miR125a | Chr19: 56887676 (+) | [56882098, 56886347] | CpG+ | none predicted | NA |
| miR-216a∼miR-217 | Chr2: 56069698 (−) | [56072783, 56074282] | CpG− | 56073933 | 3985 |
| miR-301b∼miR-130b | Chr22: 20337269 (+) | [20335283, 20337282] | CpG+ | 20336583 | 686 |
| let-7a-3∼let-7b | Chr22: 44887292 (+) | [44879283, 44883032] | CpG+ | 44881933 | 5109 |
| miR-206∼miR-133b | Chr6: 52117105 (+) | [52096878, 52098877] | CpG− | 52098453 | 18402 |
| miR-30a | Chr6: 72170045 (−) | [72164628, 72176377] | CpG− | 72174203 | 3908 |
| miR-129-1 | Chr7: 127635160 (+) | [127593752, 127595501] | CpG+ | 127594092 | 41068 |
| miR-183∼miR-96∼miR-182 | Chr7: 129202090 (−) | [129206752, 129207751] | CpG+ | 129207202 | 5112 |
| miR-29b-1∼miR-29a | Chr7: 130212838 (−) | [130219002, 130223501] | CpG− | 130223027 | 9939 |
| miR-30d∼miR-30b | Chr8: 135886370 (−) | [135913283, 135915782] | CpG+ | 135914133 | 27763 |
| let-7a-1∼let-7f-1∼let-7d | Chr9: 95978059 (+) | [95966631, 95971380] | CpG+ | 95969131 | 9928 |
| miR-181a-2∼miR-181b-2 | Chr9: 126494541 (+) | [126459631, 126464380] | CpG− | 126460831 | 33460 |
| miR-222∼miR-221 | ChrX: 45491474 (−) | [45504862, 45507861] | CpG− | 45506782 | 15308 |
| miR-542∼miR-450a-2∼miR-450a-1∼miR-450b | ChrX: 133503133 (−) | [133502362, 133506611] | CpG+ | 133505762 | 2629 |
| miR-505 | ChrX: 138834056 (−) | [138842362, 138844111] | CpG+ | 138843122 | 9066 |
miRNA: miRNA gene symbol, multiple symbols designate cluster of co-expressed miRNAs; Chromosomal location: the chromosomal position and orientation of the miRNA gene; ChIP-chip region: the nearest region with a statistically significant peak; CPPP model: the CpG (CpG+) or non-CpG (CpG−) model used for the TSS prediction; Predicted TSS: TSS predicted by CPPP; Distance: the distance of the predicted TSS from the most 5′ pre-miRNA transcript. Bold letters designate previously verified TSSs.