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5 results for “Cubaris”
Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.
Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).
Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between <i>trnS1</i> and <i>trnL1</i></td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between <i>rrnL</i> and <i>trnE</i></td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
Table 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 1.</b> Arrangement and annotation of the mitochondrial genome of Cubaris murina.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Name</th><td>Type</td><td>Start</td><td>Stop</td><td>Strand</td><td>(bp)</td><td>Start</td><td>Stop</td><td>Inter-genic space</td><td>Overlap</td></tr><tr><th>Cox1</th><td>Coding</td><td>1</td><td>1536</td><td>+</td><td>1536</td><td>ATG</td><td>TAA</td><td>1</td><td></td></tr><tr><th>trnL2(tta)</th><td>tRNA</td><td>1538</td><td>1598</td><td>+</td><td>61</td><td></td><td></td><td>48</td><td></td></tr><tr><th>Cox2</th><td>Coding</td><td>1647</td><td>2282</td><td>+</td><td>636</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnK(aaa)</th><td>tRNA</td><td>2281</td><td>2336</td><td>+</td><td>56</td><td></td><td></td><td></td><td>8</td></tr><tr><th>trnD(gac)</th><td>tRNA</td><td>2329</td><td>2403</td><td>+</td><td>75</td><td></td><td></td><td></td><td>17</td></tr><tr><th>atp8</th><td>Coding</td><td>2387</td><td>2533</td><td>+</td><td>147</td><td>ATA</td><td>TAA</td><td></td><td>4</td></tr><tr><th>atp6</th><td>Coding</td><td>2530</td><td>3192</td><td>+</td><td>663</td><td>ATA</td><td>TAA</td><td>2</td><td></td></tr><tr><th>Cox3</th><td>Coding</td><td>3195</td><td>3989</td><td>+</td><td>795</td><td>ATG</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnR(cga)</th><td>tRNA</td><td>3988</td><td>4055</td><td>+</td><td>68</td><td></td><td></td><td>55</td><td></td></tr><tr><th>nad3</th><td>Coding</td><td>4111</td><td>4407</td><td>+</td><td>297</td><td>ATA</td><td>TAA</td><td></td><td>9</td></tr><tr><th>trnA(gca)</th><td>tRNA</td><td>4399</td><td>4446</td><td>+</td><td>48</td><td></td><td></td><td></td><td>8</td></tr><tr><th>nad1 CR putative</th><td>Coding</td><td>4439 5219</td><td>5218 5360</td><td>−</td><td>780 142</td><td>ATG</td><td>TAG</td><td></td><td>14</td></tr><tr><th>NCR1</th><td>tRNA</td><td>5361</td><td>5429</td><td>+</td><td>69</td><td></td><td></td><td></td><td>17</td></tr><tr><th>rrnS</th><td>rRNA</td><td>5413</td><td>6139</td><td>+</td><td>727</td><td></td><td></td><td>48</td><td></td></tr><tr><th>trnW(tga)</th><td>tRNA</td><td>6188</td><td>6244</td><td>+</td><td>57</td><td></td><td></td><td></td><td>7</td></tr><tr><th>trnS1(aga)</th><td>tRNA</td><td>6238</td><td>6296</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR2</th><td></td><td>6297</td><td>6666</td><td></td><td>370</td><td></td><td></td><td></td><td></td></tr><tr><th>trnL1(cta)</th><td>tRNA</td><td>6667</td><td>6731</td><td>−</td><td>65</td><td></td><td></td><td>29</td><td></td></tr><tr><th>cob</th><td>Coding</td><td>6759</td><td>7907</td><td>−</td><td>1,149</td><td>ATA</td><td>TAG</td><td>38</td><td></td></tr><tr><th>trnT(aca)</th><td>tRNA</td><td>7946</td><td>8017</td><td>−</td><td>72</td><td></td><td></td><td>29</td><td></td></tr><tr><th>nad5</th><td>Coding</td><td>8047</td><td>9648</td><td>+</td><td>1,602</td><td>ATG</td><td>TAG</td><td></td><td>3</td></tr><tr><th>trnF(ttc)</th><td>tRNA</td><td>9646</td><td>9707</td><td>+</td><td>62</td><td></td><td></td><td></td><td>15</td></tr><tr><th>trnH(cac)</th><td>tRNA</td><td>9693</td><td>9758</td><td>−</td><td>66</td><td></td><td></td><td></td><td>23</td></tr><tr><th>nad4</th><td>Coding</td><td>9736</td><td>11,082</td><td>−</td><td>1,312</td><td>ATA</td><td>TAA</td><td>13</td><td></td></tr><tr><th>nad4L</th><td>Coding</td><td>11,096</td><td>11,374</td><td>−</td><td>279</td><td>ATA</td><td>TAA</td><td></td><td>13</td></tr><tr><th>trnP(cca)</th><td>tRNA</td><td>11,362</td><td>11,422</td><td>−</td><td>61</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad6</th><td>Coding</td><td>11,448</td><td>11,903</td><td>+</td><td>456</td><td>ATA</td><td>TAG</td><td></td><td>2</td></tr><tr><th>trnS2(tca)</th><td>tRNA</td><td>11,902</td><td>11,962</td><td>+</td><td>61</td><td></td><td></td><td>17</td><td></td></tr><tr><th>rrnL</th><td>rRNA</td><td>11,980</td><td>12,549</td><td>−</td><td>570</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR3</th><td></td><td>12,550</td><td>12,753</td><td></td><td>204</td><td></td><td></td><td></td><td></td></tr><tr><th>trnE(gaa)</th><td>tRNA</td><td>12,754</td><td>12,812</td><td>−</td><td>59</td><td></td><td></td><td></td><td></td></tr><tr><th>NCR4</th><td></td><td>12,813</td><td>12,950</td><td></td><td>138</td><td></td><td></td><td></td><td></td></tr><tr><th>trnV(gta)</th><td>tRNA</td><td>12,951</td><td>13,019</td><td>−</td><td>69</td><td></td><td></td><td></td><td>5</td></tr><tr><th>trnQ(caa)</th><td>tRNA</td><td>13,015</td><td>13,077</td><td>−</td><td>63</td><td></td><td></td><td></td><td>6</td></tr><tr><th>trnM(atg)</th><td>tRNA</td><td>13,072</td><td>13,141</td><td>+</td><td>70</td><td></td><td></td><td>25</td><td></td></tr><tr><th>nad2</th><td>Coding</td><td>13,167</td><td>14,123</td><td>+</td><td>978</td><td>ATA</td><td>TAG</td><td></td><td>15</td></tr><tr><th>trnC(tgc)</th><td>tRNA</td><td>14,109</td><td>14,158</td><td>−</td><td>50</td><td></td><td></td><td></td><td></td></tr><tr><th>trnY(tac)</th><td>tRNA</td><td>14,159</td><td>14,205</td><td>−</td><td>47</td><td></td><td></td><td>7</td><td></td></tr></tbody></table>
Table 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 2.</b> Base composition (%) of nucleotide, AT content, and AT- and GC-skew of the mitochondrial genome of <i>Cubaris murina.</i> Values in bold indicate positive AT-skew.</p><table><tbody><tr><th></th><th></th><th></th><th>Base composition (%)</th><th></th><th></th><th></th><th></th></tr></tbody><tbody><tr><th>Total</th><td></td><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th>14,212 bp</th><td>28.90%</td><td>15.80%</td><td>23.40%</td><td>31.90%</td><td>60.80%</td><td>−0.049</td><td>0.194</td></tr><tr><th></th><td></td><td></td><td>Base composition (%)</td><td></td><td></td><td></td><td></td></tr><tr><th>Gene Strand</th><td>A</td><td>C</td><td>G</td><td>T</td><td>%AT</td><td>AT skew</td><td>GC skew</td></tr><tr><th><i>cox1</i></th><td>(+)</td><td>22.4%</td><td>18.6%</td><td>24.2%</td><td>34.8%</td><td>57.2%</td><td>−0.217</td><td>0.131</td></tr><tr><th><i>cox2</i></th><td>(+)</td><td>20.6%</td><td>21.7%</td><td>27.7%</td><td>30.0%</td><td>50.6%</td><td>−0.186</td><td>0.121</td></tr><tr><th><i>atp8</i></th><td>(+)</td><td>21.1%</td><td>15.0%</td><td>34.7%</td><td>29.3%</td><td>50.4%</td><td>−0.163</td><td>0.396</td></tr><tr><th><i>atp6</i></th><td>(+)</td><td>20.4%</td><td>19.8%</td><td>29.1%</td><td>30.8%</td><td>51.2%</td><td>−0.203</td><td>0.190</td></tr><tr><th><i>cox3</i></th><td>(+)</td><td>17.2%</td><td>23.6%</td><td>28.6%</td><td>30.6%</td><td>47.8%</td><td>−0.280</td><td>0.096</td></tr><tr><th><i>nad3</i></th><td>(+)</td><td>20.2%</td><td>16.2%</td><td>32.3%</td><td>31.3%</td><td>51.5%</td><td>−0.216</td><td>0.332</td></tr><tr><th><i>nad1</i></th><td>(−)</td><td>31.7%</td><td>22.2%</td><td>27.6%</td><td>18.6%</td><td>50.3%</td><td><b>0.260</b></td><td>0.108</td></tr><tr><th><i>NCR1</i></th><td></td><td>28.9%</td><td>27.5%</td><td>19.7%</td><td>23.9%</td><td>52.8%</td><td>0.095</td><td>−0.165</td></tr><tr><th><i>NCR2</i></th><td></td><td>27.0%</td><td>22.2%</td><td>18.1%</td><td>32.7%</td><td>59.7%</td><td>−0.095</td><td>−0.102</td></tr><tr><th><i>cob</i></th><td>(−)</td><td>36.0%</td><td>12.0%</td><td>23.5%</td><td>28.5%</td><td>64.5%</td><td><b>0.116</b></td><td>0.324</td></tr><tr><th><i>nad5</i></th><td>(+)</td><td>28.5%</td><td>10.5%</td><td>21.7%</td><td>39.3%</td><td>67.8%</td><td>−0.159</td><td>0.348</td></tr><tr><th><i>nad4</i></th><td>(−)</td><td>38.4%</td><td>11.9%</td><td>22.8%</td><td>26.9%</td><td>65.3%</td><td><b>0.176</b></td><td>0.314</td></tr><tr><th><i>nad4L</i></th><td>(−)</td><td>41.9%</td><td>12.2%</td><td>17.6%</td><td>28.3%</td><td>70.2%</td><td><b>0.194</b></td><td>0.181</td></tr><tr><th><i>nad6</i></th><td>(+)</td><td>25.7%</td><td>10.5%</td><td>17.8%</td><td>46.1%</td><td>71.8%</td><td>−0.284</td><td>0.258</td></tr><tr><th><i>NCR3</i></th><td></td><td>36.8%</td><td>9.8%</td><td>19.1%</td><td>34.3%</td><td>71.1%</td><td>0.035</td><td>0.322</td></tr><tr><th><i>NCR4</i></th><td></td><td>35.5%</td><td>13.0%</td><td>15.2%</td><td>36.2%</td><td>71.7%</td><td>−0.010</td><td>0.078</td></tr><tr><th><i>nad2</i></th><td>(+)</td><td>28.9%</td><td>12.4%</td><td>22.6%</td><td>36.1%</td><td>65.0%</td><td>−0.111</td><td>0.291</td></tr></tbody></table>
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