Difference between revisions of "Ribosome Binding Sites/Prokaryotic/Constitutive/Anderson"

(New page: .<br> {{JCA_Arkin_RBSFamily}})
 
Line 1: Line 1:
−
[[Template:JCA_Arkin_RBSFamily | .]]<br>
+
==Description==
−
{{JCA_Arkin_RBSFamily}}
+
<partinfo>BBa_J61100 short</partinfo>
 +
 
 +
{|class="wikitable" style="border:3px solid black; width: 50%" align="center"  cellspacing="0"
 +
! style="background:grey; color:black"  |Identifier
 +
! style="background:grey; color:black"  |Sequence
 +
|-
 +
| align="center"| Master Sequence
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">NNN</font>GA<font color="red">NNN</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61100</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61101</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CAG</font>GA<font color="red">CCC</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61102</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TCC</font>GA<font color="red">TGT</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61103</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TTA</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61104</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">AGG</font>GA<font color="red">CAG</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61105</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61106</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61107</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61108</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61109</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61110</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61111</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61112</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61113</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61114</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61115</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61116</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61117</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61118</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61119</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61120</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61121</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61122</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61123</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61124</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61125</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61126</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61127</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61128</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61129</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61130</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61131</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61132</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61133</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61134</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61135</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61136</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61137</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61138</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|-
 +
|align="center"|<partinfo>J61139</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">TACTAG</font><font color="green">ATG</font></font>
 +
|}
 +
 
 +
These parts are present in plasmid pSB1A2, but there is also a constitutive promoter (J23100-derived) inserted into the XbaI site.  So, for example, the EcoRI/PstI region of part J61100 reads:
 +
  Biobrick 5'    XbaI                    J23100              XbaI    '''RBS Part'''    Biobrick 3'
 +
  gaattcgcggccgcttctagaGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCTtctaga'''GAAAGAGGGGACAA'''actagtagcggccgctgcag
 +
 
 +
This feature in no way prevents the use of these parts in standard Biobrick assembly.  Normal prefix insertion into EcoRI/XbaI will delete this promoter element.  Suffix insertion into SpeI/PstI will retain this promoter, but it can of course be removed later by a prefix insertion.
 +
 
 +
Note also that the base 5' to the SpeI site is allowed to float in these parts and is therefore rarely
 +
"T".  The "G" downstream of the XbaI site obeys the standard.  Because the database does not permit variation at this position, the predicted sequences of composite parts derived from these parts will be incorrect at this position.
 +
 
 +
More on this family of parts and their quantitative behavior is described [[JCA_Arkin_RBSFamilyPart2 | here]].

Revision as of 18:47, 6 September 2008

Description

Ribosome Binding Site Family Member

Identifier Sequence
Master Sequence TCTAGAGAAAGANNNGANNNTACTAGATG
BBa_J61100 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61101 TCTAGAGAAAGACAGGACCCTACTAGATG
BBa_J61102 TCTAGAGAAAGATCCGATGTTACTAGATG
BBa_J61103 TCTAGAGAAAGATTAGACAATACTAGATG
BBa_J61104 TCTAGAGAAAGAAGGGACAGTACTAGATG
BBa_J61105 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61106 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61107 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61108 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61109 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61110 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61111 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61112 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61113 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61114 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61115 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61116 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61117 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61118 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61119 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61120 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61121 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61122 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61123 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61124 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61125 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61126 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61127 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61128 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61129 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61130 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61131 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61132 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61133 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61134 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61135 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61136 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61137 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61138 TCTAGAGAAAGAGGGGACAATACTAGATG
BBa_J61139 TCTAGAGAAAGAGGGGACAATACTAGATG

These parts are present in plasmid pSB1A2, but there is also a constitutive promoter (J23100-derived) inserted into the XbaI site. So, for example, the EcoRI/PstI region of part J61100 reads: 

 Biobrick 5'    XbaI                    J23100              XbaI    RBS Part     Biobrick 3'
 gaattcgcggccgcttctagaGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCTtctagaGAAAGAGGGGACAAactagtagcggccgctgcag

This feature in no way prevents the use of these parts in standard Biobrick assembly. Normal prefix insertion into EcoRI/XbaI will delete this promoter element. Suffix insertion into SpeI/PstI will retain this promoter, but it can of course be removed later by a prefix insertion.

Note also that the base 5' to the SpeI site is allowed to float in these parts and is therefore rarely "T". The "G" downstream of the XbaI site obeys the standard. Because the database does not permit variation at this position, the predicted sequences of composite parts derived from these parts will be incorrect at this position.

More on this family of parts and their quantitative behavior is described here.