All discovered RREs

The following table presents all discovered RRE Motifs



Motif IDMotif IUPAC SequenceSequence LogoStudy
>1CAUAGAN COSMOS
>2UNAUGGA COSMOS
>3UYGANGA COSMOS
>4AUGUAN COSMOS
>5UYGCNGA COSMOS
>6UYCGNGA COSMOS
>7GCNCCNNNNGY COSMOS
>8NNCAGGANN COSMOS
>9CNAAGGNNG COSMOS
>10UGGCCNNNYYR COSMOS
>11NAGGCNAUN COSMOS
>12NNUYGUNNACACGANN COSMOS
>13NNNRNNAUNCUNNN COSMOS
>14ACUGGARGU COSMOS
>15NUNUUNNCNAANAN COSMOS
>16AUUUAUU COSMOS
>17NNUNAANCCANN COSMOS
>18NNGANCCAYNN COSMOS
>19YUUYRNNAUGAAG COSMOS
>20CGNAUCNNNNNYG COSMOS
>21YUGYRNNCUGCAG COSMOS
>22CAGGGNNNYUG COSMOS
>23NCGUNGURYGN COSMOS
>24AGUCNGNNNNRYU COSMOS
>25GNCUCNAC COSMOS
>26NRGURNNUNUACUN COSMOS
>27YUGAGCAG COSMOS
>28UUCGCCNGRR COSMOS
>29ANCGNGNNYGNU COSMOS
>30NNRNGGNNUCCNUNN COSMOS
>31YNGNNNUGCCNG COSMOS
>32GYRRNCUUUGC COSMOS
>33NNRNAAGUCUNN COSMOS
>34NUUGCNNNNNNNNNNNGYRRN COSMOS
>35NNNAANAANNNNUNUUNNN COSMOS
>36UAUUURKYY GRAFFER
>37KYNUAKCGK GRAFFER
>38ANWRUUAUR GRAFFER
>39WAUWUGKWW GRAFFER
>40UAUUYYUKK GRAFFER
>41AUAURUWKR GRAFFER
>42AUSMUSAYK GRAFFER
>43SYCYMSCCC GRAFFER
>44UWKUGGSAW GRAFFER
>45MUSNGWGAR GRAFFER
>46KGNMUGNUW GRAFFER
>47KYUYSUUMG GRAFFER
>48UUUKUUUMK GRAFFER
>49RRYRGUGCW GRAFFER
>50MKWUYCAWG GRAFFER
>51GYGWASGNR GRAFFER
>52MCWCWSUGS GRAFFER
>53UUAUKWWMR GRAFFER
>54UUCYNUMU GRAFFER
>55RNMURWGAG GRAFFER
>56SUWCUUWAR GRAFFER
>57SAYACYNC GRAFFER
>58ACAKCCAM GRAFFER
>59WYWUGUGCY GRAFFER
>60YUAGRUC GRAFFER
>61CUUUKRGNK GRAFFER
>62YCNSCUG GRAFFER
>63SCCRUWUSS GRAFFER
>64AWGNUNCRC GRAFFER
>65RNASAAUYW GRAFFER
>66UUMCUWRNY GRAFFER
>67CUCWYUUU GRAFFER
>68KAWAAMGW GRAFFER
>69SWRGAGAK GRAFFER
>70YGUUNUUGY GRAFFER
>71CKWWUAGSA GRAFFER
>72UUWUUAUKA GRAFFER
>73GCKUGCNSY GRAFFER
>74WYYUUCCNS GRAFFER
>75WUWUCWYAR GRAFFER
>76UUMWSUUNW GRAFFER
>77WWAWAYWAU GRAFFER
>78SNKCGRWCG GRAFFER
>79KANUMCCMC GRAFFER
>80KWUANYGGR GRAFFER
>81YGWUNGKUY GRAFFER
>82UNCAGSWUK GRAFFER
>83URAWKCANW GRAFFER
>84CSSYAGCRS GRAFFER
>85CSAMMUGK GRAFFER
>86WWUUUYAKU GRAFFER
>87RCUCCNCMS GRAFFER
>88GRCCRUWUK GRAFFER
>89SNUUGCUMG GRAFFER
>90KWAGWKCAY GRAFFER
>91UANKGARUY GRAFFER
>92AKCRAAWMK GRAFFER
>93KUSCRGUGY GRAFFER
>94RGKGACWAW GRAFFER
>95UKURCKUKK GRAFFER
>96CUYAAMKSU GRAFFER
>97AUMRCWCNR GRAFFER
>98KNGSCGWCS GRAFFER
>99MYCGUAAW GRAFFER
>100KYNSCUKAU GRAFFER
>101YYAKUUYNG GRAFFER
>102WKKGAWAGS GRAFFER
>103WNAYSGUKC GRAFFER
>104SKUGKSUSU GRAFFER
>105UNRAUAMA GRAFFER
>106GNYAYUUWW GRAFFER
>107CMRUWAUS GRAFFER
>108ARGGSAGNS GRAFFER
>109CWUNRGCY GRAFFER
>110KGRCNGSU GRAFFER
>111KUUWSRGUR GRAFFER
>112MNUGAGANR GRAFFER
>113AAAWCKSNM GRAFFER
>114WANARAYGK GRAFFER
>115AAWUWANWW GRAFFER
>116YUSUMAYC GRAFFER
>117KWSUAUUWK GRAFFER
>118MRNGWAGCA GRAFFER
>119KNGWCCMWU GRAFFER
>120CMMMAUAYR GRAFFER
>121CRGGKKG GRAFFER
>122URCAKANWM GRAFFER
>123MUCCAKRMR GRAFFER
>124RMCAUAGAW GRAFFER
>125CAUAGAGRN GRAFFER
>126KYAUAGAWW GRAFFER
>127CUAGAUNNK GRAFFER
>128KNUYAUAGA GRAFFER
>129NDMUGCCRK fRNAs
>130GMMUVGCUW fRNAs
>131HUAAKRKYM fRNAs
>132NACAUKAUD fRNAs
>133KCUMMUAYH fRNAs
>134YAUCUGKCB fRNAs
>135DCGKUCCUS fRNAs
>136WCUUUUKCN fRNAs
>137VACYAKACD fRNAs
>138HCCGUCUAY fRNAs
>139VAGAAMAWD fRNAs
>140DVRKAAUUCY fRNAs
>141NCSCACGVH fRNAs
>142KUAHYRUGR fRNAs
>143NUSCUYUAD fRNAs
>144MUGGVACAK fRNAs
>145CACGUCAGY fRNAs
>146RUUCKGUCS fRNAs
>147HUACGUUCN fRNAs
>148HGVUAAGCV fRNAs
>149VGGGCCRCV fRNAs
>150CAUWGUD RNAcompete
>151CUKUUKY RNAcompete
>152NDUUAUHN RNAcompete
>153NUAUACUN RNAcompete
>154CUUUCUN RNAcompete
>155KUWCACG RNAcompete
>156NGAAGGDN RNAcompete
>157HUUCACR RNAcompete
>158WGUAGRW RNAcompete
>159ARAAANA RNAcompete
>160AAAMAAA RNAcompete



References:


  1. COSMOS:
    Global identification of conserved post-transcriptional regulatory programs in trypanosomatids
    Najafabadi, H. S., Lu, Z., Macpherson, C., Mehta, V., Adoue, V., Pastinen, T., and Salavati, R.
    Nucleic Acids Res, 2013
  2. GRAFFER:
    Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei
    Gazestani, V. H., and Salavati, R.
    PLoS One, 2015
  3. Genome-wide functional RNAs(fRNAs):
    Genome-wide computational identification of functional RNA elements in Trypanosoma brucei
    Mao, Y., Najafabadi, H. S., and Salavati, R.
    BMC Genomics, 2009
  4. RNAcompete:
    A compendium of RNA-binding motifs for decoding gene regulation
    Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., Na, H., Irimia, M., Matzat, L. H., Dale, R. K., Smith, S. A., Yarosh, C. A., Kelly, S. M., Nabet, B., Mecenas, D., Li, W., Laishram, R. S., Qiao, M., Lipshitz, H. D., Piano, F., Corbett, A. H., Carstens, R. P., Frey, B. J., Anderson, R. A., Lynch, K. W., Penalva, L. O., Lei, E. P., Fraser, A. G., Blencowe, B. J., Morris, Q. D., and Hughes, T. R.
    Nature, 2013