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