Table 4.
sRNA candidates identified in previous studies
| ID | Type | Position | St. | Size | Rfam | St. | Ov. | ID [36] | St. | Ov. | ID [37] | St. | ID [38] | St. | Ov. | North. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SmelC011 | 3 | 46011-46166 | - | 156 | sra02 | n | ||||||||||
| SmelC023 | 1 | 201679-201825 | + | 147 | C7 | + | 100 | sra03 | + | SmrC7 | + | 98 | [37-39] | |||
| SmelC035 | 2 | 259927-260032 | + | 106 | RF00169 | + | 97 | sra05 | + | |||||||
| SmelC037 | 3 | 267059-267152 | + | 94 | Sm76 | + | 59 | [39] | ||||||||
| SmelC051 | 3 | 318407-318497 | + | 91 | sra09 | n | ||||||||||
| SmelC057 | 4 | 364136-364231 | - | 96 | Sm134 | + | 32 | |||||||||
| SmelC073 | 1 | 424110-424268 | + | 159 | Sm131 | + | 72 | |||||||||
| SmelC089 | 3 | 523807-524015 | + | 209 | Sm39 | + | 33 | |||||||||
| SmelC100 | 3 | 580087-580184 | - | 98 | RF00521 | - | 76 | sra13 | n | |||||||
| SmelC116 | 2 | 658552-658723 | - | 172 | Sm105 | - | 49 | |||||||||
| SmelC119 | 1 | 701950-702109 | + | 160 | sra16 | - | ||||||||||
| SmelC132 | 3 | 757653-757739 | + | 87 | Sm139 | + | 100 | |||||||||
| SmelC213 | 2 | 1048676-1048864 | + | 189 | sra25 | + | [38,39] | |||||||||
| SmelC222 | 3 | 1071388-1071540 | - | 153 | Sm145 | - | 67 | [39] | ||||||||
| SmelC226 | 1 | 1091100-1091291 | + | 192 | Sm10 | + | 100 | |||||||||
| SmelC246 | 3 | 1238618-1238804 | - | 187 | sra29 | - | [38] | |||||||||
| SmelC289 | 1 | 1398278-1398426 | - | 149 | C9 | - | 81 | sra32 | - | SmrC9 | - | 99 | [37-39] | |||
| SmelC291 | 1 | 1411678-1411848 | + | 171 | C10 | + | 77 | sra33 | + | [38] | ||||||
| SmelC302 | 3 | 1458322-1458424 | + | 103 | sra34 | - | [38] | |||||||||
| SmelC306 | 4 | 1461414-1461561 | + | 148 | sra35 | + | ||||||||||
| SmelC311 | 3 | 1464122-1464318 | + | 197 | sra36 | + | ||||||||||
| SmelC337 | 1 | 1518791-1518985 | + | 195 | Sm30 | + | 100 | |||||||||
| SmelC365 | 4 | 1599106-1599255 | + | 150 | Sm55 | - | 24 | |||||||||
| SmelC378 | 4 | 1635062-1635243 | + | 182 | Sm9 | - | 15 | |||||||||
| SmelC381 | 1 | 1637121-1637244 | + | 124 | sra37 | - | Sm50 | - | 48 | |||||||
| SmelC397 | 1 | 1667491-1667614 | - | 124 | C14 | - | 100 | SmrC14 | - | 100 | [37] | |||||
| SmelC398 | 1 | 1667766-1667982 | - | 217 | sra38 | n | Sm7 | - | 99 | |||||||
| SmelC411 | 1 | 1698618-1698731 | - | 114 | RF00519 | - | 62 | C15 | - | 100 | SmrC15 | - | 100 | [37] | ||
| SmelC412 | 1 | 1698818-1698948 | - | 131 | RF00519 | - | 57 | C16 | - | 100 | sra41 | n | SmrC16 | - | 98 | [37,38] |
| SmelC414 | 3 | 1706675-1706765 | - | 91 | Sm23 | - | 56 | |||||||||
| SmelC416 | 1 | 1718814-1718919 | - | 106 | Sm138 | - | 85 | |||||||||
| SmelC419 | 5 | 1728029-1728277 | - | 249 | Sm6 | - | 97 | |||||||||
| SmelC434 | 1 | 1821211-1821366 | + | 156 | Sm118 | + | 100 | |||||||||
| SmelC435 | 1 | 1823103-1823231 | + | 129 | Sm48 | + | 100 | |||||||||
| SmelC445 | 3 | 1879868-1879947 | - | 80 | sra44 | n | ||||||||||
| SmelC475 | 1 | 2059726-2059795 | - | 70 | Sm29 | - | 100 | |||||||||
| SmelC483 | 1 | 2098461-2098583 | - | 123 | C17 | + | 100 | |||||||||
| SmelC488 | 1 | 2129185-2129292 | - | 108 | Sm135 | - | 99 | |||||||||
| SmelC525 | 1 | 2291226-2291466 | + | 241 | sra49 | + | ||||||||||
| SmelC531 | 2 | 2321050-2321287 | - | 238 | Sm26 | - | 98 | [39] | ||||||||
| SmelC549 | 1 | 2371597-2371855 | + | 259 | Sm4 | + | 99 | |||||||||
| SmelC559 | 4 | 2398177-2398336 | + | 160 | RF00050 | + | 100 | C20 | + | 91 | ||||||
| SmelC561 | 4 | 2436481-2436577 | + | 97 | Sm52 | - | 100 | |||||||||
| SmelC576 | 4 | 2524155-2524249 | + | 95 | Sm136 | - | 27 | |||||||||
| SmelC587 | 3 | 2575832-2575947 | - | 116 | Sm104 | - | 67 | |||||||||
| SmelC617 | 1 | 2695496-2695642 | - | 147 | Sm49 | - | 100 | |||||||||
| SmelC642 | 3 | 2921789-2922084 | + | 296 | sra54 | n | ||||||||||
| SmelC646 | 3 | 2924467-2924555 | - | 89 | sra55 | n | ||||||||||
| SmelC653 | 3 | 2937985-2938127 | - | 143 | RF00517 | - | 34 | |||||||||
| SmelC667 | 2 | 2972090-2972252 | - | 163 | RF00013 | - | 98 | C22 | - | 83 | sra56 | - | [37-39] | |||
| SmelC671 | 1 | 2986421-2986520 | + | 100 | Sm84 | + | 100 | [39] | ||||||||
| SmelC689 | 1 | 3046710-3046789 | + | 80 | RF00519 | + | 81 | Sm8 | + | 96 | [39] | |||||
| SmelC691 | 1 | 3048822-3048904 | + | 83 | sra57 | n | ||||||||||
| SmelC706 | 1 | 3105298-3105445 | - | 148 | RF00518 | - | 100 | C45 | - | 52 | [37] | |||||
| SmelC752 | 3 | 3439569-3439771 | + | 203 | sra67 | + | ||||||||||
| SmelC762 | 3 | 3461772-3461886 | + | 115 | RF00521 | + | 63 | |||||||||
| SmelC764 | 4 | 3472924-3473053 | + | 130 | RF00519 | + | 44 | |||||||||
| SmelC778 | 1 | 3522269-3522383 | + | 115 | Sm5 | + | 97 | |||||||||
| SmelC779 | 3 | 3532867-3532968 | + | 102 | RF00059 | + | 100 | |||||||||
| SmelC804* | 1 | 1599291-1599363 | 73 | Sm55 | - | 73 | ||||||||||
| SmelC805* | 1 | 1677330-1677472 | 143 | sra40 | n | |||||||||||
| SmelC809* | 1 | 2356793-2357134 | 342 | RF00010 | - | 100 | C19 | - | 100 | sra50 | + | |||||
| SmelA033 | 1 | 512140-512221 | - | 82 | A2 | + | 100 | smA3a | - | 83 | ||||||
| SmelA035 | 1 | 552854-552983 | + | 130 | RF00519 | + | 55 | smA4b | + | 98 | ||||||
| SmelA075 | 1 | 1220693-1220808 | + | 116 | smA8 | + | 99 | |||||||||
| SmelA099 | 1 | 1328175-1328334 | - | 160 | A6 | + | 100 | |||||||||
| SmelA102 | 3 | 1351156-1351309 | - | 154 | RF00490 | - | 43 | |||||||||
| SmelA103 | 2 | 1351298-1351357 | + | 60 | RF00489 | + | 73 | |||||||||
| SmelB001 | 1 | 24911-24992 | - | 82 | B29 | + | 100 | |||||||||
| SmelB006 | 2 | 56486-56620 | + | 135 | RF00489 | + | 35 | B30 | + | 52 | ||||||
| SmelB011 | 1 | 66261-66326 | + | 66 | RF00174 | + | 100 | B31 | + | 21 | ||||||
| SmelB019 | 1 | 213497-213616 | + | 120 | smB1 | + | 93 | |||||||||
| SmelB027 | 2 | 334403-334483 | - | 81 | B34 | + | 100 | |||||||||
| SmelB032 | 1 | 379136-379275 | + | 140 | smB2 | + | 91 | |||||||||
| SmelB044 | 1 | 541771-541909 | - | 139 | smB3b | - | 100 | |||||||||
| SmelB050 | 1 | 574628-574763 | + | 136 | smB5a | + | 100 | |||||||||
| SmelB053 | 1 | 577730-577873 | + | 144 | B35 | + | 99 | smrB35 | + | 97 | [37] | |||||
| SmelB085 | 3 | 871959-872147 | - | 189 | RF00435 | - | 50 | |||||||||
| SmelB110 | 2 | 1192051-1192144 | - | 94 | RF00059 | - | 100 | |||||||||
| SmelB126 | 1 | 1325476-1325586 | + | 111 | smB9 | + | 100 | |||||||||
| SmelB169 | 1 | 1633737-1633873 | + | 137 | RF00059 | + | 80 |
Overlap, percent overlap of the candidates from the cited studies or database compared to the region covered by a sRNA candidate in this study. n, strand was not or not undoubtedly determined.
ID; RNA ID (this study); Type, RNA type; St., strand; Ov., overlap (%); ID [], RNA ID corresponding to the given reference; North., experimentally validated by Northern blot, given are the references for the Northern hybridizations. RNA ID: *, Solexa candidate. RNA type: 1, trans-encoded sRNA; 2, cis-encoded antisense sRNA; 3, mRNA leader; 4, sense sRNA; 5, Open reading frame. The presumed location of the sRNAs predicted by Ulvé et al. [37], derived from the location of the Dot Blot probes. Thus an overlap analysis to our candidates could not be performed.