Table 2. MapMi homology mapping of P. hawaiensis conserved miRNA to the Daphnia pulex genome.
mirBasemiRNA | Query sequence | Mismatch | Chromosome | start | end | length | MapMi Score |
mir-1 | TGGAATGTAAAGAAGTATGGAGC | 0 | scaffold_1 | 1720882 | 1720904 | 23 | 48.27 |
mir-2a | TATCACAGCCAGCTTTGATGAGC | 0 | scaffold_80 | 241083 | 241105 | 23 | 54.12 |
mir-12 | TGAGTATTACATCAGGTACTGGT | 0 | scaffold_1 | 1847883 | 1847905 | 23 | 47.86 |
mir-34 | TGGCAGTGTGGTTAGCTGGT | 0 | scaffold_4 | 1242095 | 1242114 | 20 | 52.09 |
mir-71 | TGAAAGACATGGGTAGTGAGATG | 0 | scaffold_80 | 240430 | 240452 | 23 | 57.26 |
mir-79 | ATAAAGCTAGGTTACCAAAG | 0 | scaffold_2 | 1526251 | 1526270 | 20 | 51.97 |
mir-92 | AATTGCACTCGTCCCGGCCTGT | 1 | scaffold_38 | 876194 | 876215 | 22 | 35.05 |
mir-193 | ACTGGCCTGCTAAGTCCCAA | 0 | scaffold_167 | 85458 | 85477 | 20 | 46.75 |
mir-252a | CTAAGTACTGGTGCCGCAGGAG | 1 | scaffold_285 | 66066 | 66087 | 22 | 37.02 |
mir-263b | AATGGCACTGGAAGAATTCAC | 0 | scaffold_87 | 475620 | 475640 | 21 | 31.44 |
mir-263a | CTTGGCACTGGAAGAATTCACA | 0 | scaffold_87 | 475817 | 475838 | 22 | 45.22 |
mir-276 | AGGAACTTCATACCGTGCTCTC | 0 | scaffold_15 | 755668 | 755689 | 22 | 42.58 |
mir-279 | ATGACTAGATCCACACTC | 0 | Scaffold_63 | 523658 | 523675 | 18 | 35.68 |
mir-307 | TCACAACCTCCTTGAGTG | 0 | Scaffold_47 | 601105 | 641122 | 18 | 33.14 |
mir-317 | TGAACACAGCTGGTGGTATCTCA | 0 | scaffold_4 | 1243963 | 1243985 | 23 | 52.54 |
mir-745 | GAGCTGCCCAGTGAAGGGCA | 1 | scaffold_63 | 361999 | 362018 | 20 | 34.70 |
mir-965 | TAAGCGTATGGCTTTTCCCCT | 0 | scaffold_32 | 27783 | 27803 | 21 | 48.07 |
mir-993 | GAAGCTCGTTTCTACAGGTATCT | 0 | scaffold_7 | 282360 | 282382 | 23 | 49.27 |
mir-iab-4-5p | ACGTATACTGAATGTATCCTGA | 0 | scaffold_7 | 515547 | 515568 | 22 | 44.98 |
mir-iab-4-3p | CGGTATACCTTCAGTATACGTA | 0 | scaffold_7 | 515582 | 515603 | 22 | 42.92 |
bantam | GAGATCATTGTGAAAGCTGAT | 0 | scaffold_115 | 370210 | 370230 | 21 | 44.47 |
mir-275 | TCAGGTACCTGATGTAGCG | 1 | scaffold_4 | 1790782 | 1790800 | 19 | 44.53 |
Table shows the result of MapMi homology mapping to the D. pulex genome with P. hawaiensis sequences annotated by known miRNA from mirBase with a tolerance of a 1 bp mismatch. The mapping position on the D. pulex chromosome corresponding to known miRNA sequences are shown with the calculated MapMi score for the mapping and RNA fold analysis.