Table 2.
miRNAs identified in Cx. quinquefasciatus adult female mosquitoes.
| Culex | # miRNA | # miRNA* | Sequence | Length | aga | ame | dme | supercontig | Start | End | Strand |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 184 | 107190 | 0 | UGGACGGAGAACUGAUAAGGGC | 22 | Y | Y | Y | 3.567 | 240312 | 240333 | Minus |
| 317-1 | 71313 | 2 | UGAACACAGCUGGUGGUAUCU | 21 | Y | Y | Y | 3.36 | 1133209 | 1133229 | Plus |
| 317-2 | - | - | UGAACACAGCUGGUGGUAUCU | 21 | Y | Y | Y | 3.36 | 1134875 | 1134895 | Plus |
| 277 | 58628 | 0 | UAAAUGCACUAUCUGGUACGAC | 22 | Y | Y | Y | 3.36 | 1153785 | 1153806 | Plus |
| 1 | 36084 | 0 | UGGAAUGUAAAGAAGUAUGGAG | 22 | Y | Y | Y | 3.78 | 246250 | 246271 | Plus |
| 989 | 23667 | 0 | UGUGAUGUGACGUAGUGGUAC | 21 | Y | ? | Y | 3.315 | 321364 | 321384 | Plus |
| 275 | 13910 | 2 | UCAGGUACCUGAAGUAGCGC | 20 | Y | Y | Y | 3.291 | 329815 | 329834 | Plus |
| 957 | 11682 | 0 | UGAAACCGUCCAAAACUGAGGC | 22 | Y | ? | Y | 3.787 | 29593 | 29614 | Plus |
| 8-3p | 10950 | - | UAAUACUGUCAGGUAAAGAUGU | 22 | Y | Y | Y | 3.40 | 815865 | 815886 | Minus |
| 281 | 9322 | 95 | AAGAGAGCUAUCCGUCGACAGU | 22 | Y | Y | Y | 3.64 | 99744 | 99765 | Plus |
| Let-7 | 9266 | 5 | UGAGGUAGUUGGUUGUAUAGU | 21 | Y | Y | Y | 3.4 | 280610 | 280630 | Plus |
| 34 | 6301 | 3 | UGGCAGUGUGGUUAGCUGGUU | 21 | Y | Y | Y | 3.36 | 1154478 | 1154498 | Plus |
| 263 | 3749 | 2 | AAUGGCACUGGAAGAAUUCACGG | 23 | Y | Y | Y | 3.219 | 351848 | 351870 | Minus |
| 252-1 | 3157 | 2 | (C)UAAGUACUAGUGCCGCAGGAG | 21 | Y | Y | Y | 3.1787 | 6836 | 6856 | Minus |
| 252-2 | - | - | (C)UAAGUACUAGUGCCGCAGGAG | 21 | Y | Y | Y | 3.975 | 115594 | 115614 | Plus |
| 87 | 2364 | 0 | GUGAGCAAAUUUUCAGGUGUGU | 22 | Y | Y | Y | 3.431 | 379788 | 379809 | Plus |
| 71 | 2232 | 14 | AGAAAGACAUGGGUAGUGAGAU | 22 | ? | Y | ? | 3.366 | 117552 | 117573 | Minus |
| bantam-5p | 1459 | - | CCGGUUUUCAUUUUCGAUCUGAC | 21 | Y | Y | Y | 3.65 | 199737 | 199759 | Minus |
| 9 | 1138 | 440 | UCUUUGGUAUUCUAGCUGUAGA | 22 | Y | Y | Y | 3.83 | 64733 | 64754 | Plus |
| 11 | 888 | 5 | CAUCACAGUCUGAGUUCUUGCU | 22 | Y | ? | Y | 3.153 | 639669 | 639690 | Minus |
| 276-1 | 860 | 2 | UAGGAACUUCAUACCGUGCUCU | 22 | Y | Y | Y | 3.136 | 340911 | 340932 | Plus |
| 276-2 | - | - | UAGGAACUUCAUACCGUGCUCU | 22 | Y | Y | Y | 3.136 | 541192 | 541213 | Plus |
| 276-3 | - | - | UAGGAACUUCAUACCGUGCUCU | 22 | Y | Y | Y | 3.2457 | 930 | 951 | Plus |
| 210.1 | 720 | 5 | UUGUGCGUGUGACAACGGCUAU | 22 | Y | Y | Y | 3.549 | 157657 | 157678 | Minus |
| 927 | 703 | 21 | CAAAGCGUUUGGAUUCUGAAAC | 22 | Y | Y | Y | 3.11 | 560282 | 560302 | Plus |
| bantam-3p | 689 | - | UGAGAUCAUUUUGAAAGCUGA | 21 | Y | Y | Y | 3.65 | 199698 | 199718 | Minus |
| 8-5p | 594 | - | CAUCUUACCGGGCAGCAUUAGA | 22 | Y | Y | Y | 3.40 | 815904 | 815925 | Minus |
| 2 | 547 | 2 | UAUCACAGCCAGCUUUGAAGAGC | 23 | Y | Y | Y | 3.366 | 116861 | 116883 | Minus |
| 998 | 434 | 0 | UAGCACCAUGAGAUUCAGC | 19 | ? | ? | Y | 3.153 | 639527 | 639545 | Minus |
| 210.2 | 405 | - | CUUGUGCGUGUGACAACGGCUAU | 23 | Y | Y | Y | 3.549 | 157657 | 157679 | Minus |
| 14 | 358 | 0 | UCAGUCUUUUUCUCUCUCCUAU | 22 | Y | Y | Y | 3.676 | 52251 | 52272 | Minus |
| 285 | 324 | 5 | UAGCACCAUUCGAAAUCAGUAC | 22 | ? | ? | Y | 3.98 | 262290 | 262311 | Minus |
| 1890 | 287 | 0 | UGAAAUCUUUGAUUAGGUCUGG | 22 | Y | ? | ? | 3.64 | 982786 | 982807 | Minus |
| 190-1 | 231 | 0 | AGAUAUGUUUGAUAUUCUUGGUUG | 24 | Y | Y | Y | 3.181 | 347953 | 347976 | Minus |
| 190-2 | - | - | AGAUAUGUUUGAUAUUCUUGGUUG | 24 | Y | Y | Y | 3.351 | 105098 | 105121 | Minus |
| 283 | 224 | 0 | CAAUAUCAGCUGGUAAUUCUGGG | 23 | Y | Y | Y | 3.57 | 559462 | 559484 | Plus |
| 7 | 192 | 0 | UGGAAGACUAGUGAUUUUGUUGU | 23 | Y | Y | Y | 3.1 | 3357390 | 3357412 | Minus |
| 100 | 170 | 43 | AACCCGUAGAUCCGAACUUGUG | 22 | Y | Y | Y | 3.4 | 271414 | 271435 | Plus |
| 1891 | 167 | 1 | UGAGGAGUUAAUUUGCGUGUUU | 22 | Y | ? | ? | 3.829 | 180383 | 180404 | Minus |
| 999 | 165 | 0 | UGUUAACUGUAAGACUGUGUCU | 22 | ? | ? | Y | 3.14 | 96917 | 96938 | Plus |
| 309 | 33 | 1 | UCACUGGGCAUAGUUUGUCGCAU | 23 | Y | ? | Y | 3.145 | 66041 | 66063 | Minus |
| 375 | 144 | 0 | UUUGUUCGUUUGGCUCGAGUUAC | 23 | Y | Y | Y | 3.455 | 42584 | 42605 | Plus |
| 306 | 143 | 65 | UCAGGUACUGAGUGACUCUCAG | 22 | Y | ? | Y | 3.83 | 80436 | 80457 | Plus |
| 125 | 140 | 7 | UCCCUGAGACCCUAACUUGUGA | 22 | Y | Y | Y | 3.4 | 280975 | 280996 | Plus |
| 315 | 131 | 0 | UUUUGAUUGUUGCUCAGAAAGC | 22 | Y | Y | Y | 3.438 | 61926 | 61947 | Plus |
| 124 | 105 | 0 | UAAGGCACGCGGUGAAUGC | 19 | Y | Y | Y | 3.8 | 2074772 | 2074790 | Plus |
| 92b | 96 | 0 | AAUUGCACUUGUCCCGGCCUG | 21 | Y | Y | Y | 3.722 | 164913 | 164933 | Minus |
| 1889-5p | 89 | - | UAAUCUCAAAUUGUAACAGUGG | 22 | Y | ? | ? | 3.57 | 562555 | 562576 | Plus |
| 981-1 | 82 | 0 | UUCGUUGUCGACGAAACCUGCA | 22 | Y | Y | Y | 3.431 | 144482 | 144503 | Plus |
| 981-2 | - | - | UUCGUUGUCGACGAAACCUGCA | 22 | Y | Y | Y | 3.431 | 151371 | 151392 | Plus |
| 12 | 80 | 2 | UGAGUAUUACAUCAGGUACUGGU | 23 | Y | Y | Y | 3.57 | 563009 | 563031 | Plus |
| 31 | 76 | 2 | UGGCAAGAUGUUGGCAUAGCUGA | 23 | ? | Y | Y | 3.559 | 256577 | 256599 | Minus |
| 10 | 59 | 40 | CAAAUUCGGUUCUAGAGAGGUUU | 23 | Y | Y | Y | 3.12 | 96000 | 96022 | Minus |
| 1174 | 58 | 0 | CUGGGUAUUUUAGAUCAUCGGC | 22 | Y | ? | ? | 3.86 | 865901 | 865922 | Plus |
| **2945 | 52 | 0 | UGACUAGAGGCAGACUCGUUU | 20 | Y | ? | ? | 3.4 | 184461 | 184481 | Plus |
| 1000 | 49 | 0 | AUAUUGUCCUGUCACAGCAGU | 21 | Y | Y | Y | 3.153 | 102853 | 102873 | Minus |
| 13 | 37 | 3 | UAUCACAGCCAUUUUGACGAGU | 22 | Y | Y | Y | 3.366 | 116994 | 117015 | Minus |
| 996 | 36 | 2 | UGACUAGAUUACAUGCUCGU | 20 | Y | Y | Y | 3.19 | 1437010 | 1437029 | Minus |
| 137 | 33 | 0 | UAUUGCUUGAGAAUACACGUAG | 22 | Y | Y | Y | 3.1714 | 27566 | 27587 | Minus |
| 133 | 32 | 0 | UUGGUCCCCUUCAACCAGCUGU | 22 | Y | Y | Y | 3.1189 | 55748 | 55769 | Plus |
| 1175 | 35 | 7 | AAGUGGAGUAGUGGUCUCAUCG | 22 | Y | ? | ? | 3.86 | 866116 | 866137 | Plus |
| 279 | 26 | 21 | UGACUAGAUCCACACUCAUUAA | 22 | Y | Y | Y | 3.19 | 1441123 | 1441144 | Minus |
| 92a | 24 | - | UAUUGCACUUGUCCCGGCCUAU | 22 | Y | Y | Y | 3.722 | 174912 | 174933 | Minus |
| 932-3p | 22 | - | UGCAAGCAAUGUGGAAGUGA | 22 | ? | Y | Y | 3.261 | 301413 | 301432 | Minus |
| 970 | 20 | 0 | UCAUAAGACACACGCGGCUAU | 21 | Y | ? | Y | 3.495 | 35970 | 35990 | Plus |
| 316 | 18 | 0 | UGUCUUUUUCCGCUUACUGCCG | 22 | ? | Y | Y | 3.496 | 152508 | 152529 | Minus |
| 305 | 17 | 1 | AUUGUACUUCAUCAGGUGCUCU | 22 | Y | Y | Y | 3.291 | 339134 | 339155 | Plus |
| **2944a-1 | 13 | 1 | GAAGGAACUUCUGCUGUGAUC | 21 | Y | ? | ? | 3.66 | 328681 | 328701 | Minus |
| **2944a-2 | - | - | GAAGGAACUUCUGCUGUGAUC | 21 | Y | ? | ? | 3.145 | 66240 | 66260 | Minus |
| 988 | 11 | 5 | CCCUUGUUGCAAACCUCACGC | 21 | Y | ? | Y | 3.791 | 14331 | 14351 | Plus |
| 932-5p | 11 | - | UCAAUUCCGUAGUGCAUUGCAG | 22 | ? | Y | Y | 3.261 | 301450 | 301471 | Minus |
| 1889-3p | 7 | - | CACGUUACAGAUUGGGGUUUCC | 22 | Y | ? | ? | 3.57 | 562642 | 562663 | Plus |
| 993 | 4 | 1 | UACCCUGUAGUUCCGGGCUUUU | 22 | Y | Y | Y | 3.12 | 55487 | 55508 | Plus |
| 278 | 3 | 0 | UCGGUGGGACUUUCGUCCGUUU | 22 | Y | Y | Y | 3.16 | 1026212 | 1026233 | Plus |
| 965 | 2 | 0 | UAAGCGUAUAGCUUUUCCCAUU | 22 | Y | ? | Y | 3.48 | 484177 | 484198 | Plus |
| Iab-4 | 2 | 1 | ACGUAUACUGAAUGUAUCCUGA | 22 | Y | Y | Y | 3.12 | 681163 | 681184 | Plus |
| 980 | 2 | 0 | UAGCUGCCUAGUGAAGGGC | 19 | ? | ? | Y | 3.263 | 352922 | 352940 | Plus |
| 308 | 3 | 1 | CGCAGUAUAUUCUUGUGGCUUG | 22 | Y | ? | Y | 3.98 | 764133 | 764154 | Plus |
| 79 | 2 | 0 | GCUUUGGCGCUUUAGCUGUAUGA | 23 | Y | Y | Y | 3.83 | 80591 | 80613 | Plus |
| **2943 | 1 | 0 | UAAGUAGGCACUUGCAGGCAAAG | 23 | Y | ? | ? | 3.121 | 94164 | 94186 | Minus |
| **2944b-1 | 1 | 0 | GAAGGAACUCCCGGUGUGAUAU | 22 | Y | ? | ? | 3.66 | 328838 | 328859 | Minus |
| **2944b-2 | - | - | GAAGGAACUCCCGGUGUGAUAU | 22 | Y | ? | ? | 3.145 | 66389 | 66410 | Minus |
| 33 | predicted | GUGCAUUGUAGUUGCAUUGCA | 21 | ? | Y | Y | 3.1258 | 69381 | 69401 | Minus | |
| 2951 | 162309 | 342 | AAGAGCUCAGCACGCAGGGGUGGC | 24 | ? | ? | ? | multiple | |||
| 2952 | 2203 | - | UAGUACGGCCAUGACUGAGGGC | 22 | ? | ? | ? | 3.5 | 753922 | 753943 | Minus |
| 2941-1 | 1221 | 3 | UAGUACGGCUAGAACUCCACGG | 22 | ? | ? | ? | 3.5 | 753643 | 753664 | Minus |
| 2941-2 | - | 1 | UAGUACGGCUAGAACUCCACGG | 22 | ? | ? | ? | 3.5 | 753797 | 753818 | Minus |
aga = An. gambiae; ame = Ap. mellifera; dme = D. melanogaster.
Top group: miRNAs and miRNA* strands identified by deep sequencing
Middle group: predicted miR-33 was identified in C7/10 cells but absent from Cx. quinquefasciatus. miR-33 was cross-referenced with the Cx. quinquefasciatus genome.
Bottom group: novel miRNAs identified in this study.
** novel miRNAs (not present in miRBase v14) recently identified in Ae. aegypti mosquitoes while this manuscript was under review