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Table 4 sRNA candidates identified in previous studies

From: A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

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 [3739]
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 [3739]
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 -     [3739]
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          
  1. 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.
  2. 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.