KRABopedia - The place to find Krab Zinc Finger information

<u>Section list:</u> <ul> <li><a href='#General'>General</a></li> <li><a href='#Polymorphism'>Polymorphism</a></li> <li><a href='#Expression in tissues (from GTEx)'>Expression in tissues (from GTEx)</a></li> <li><a href='#CisBP motifs'>CisBP motifs</a></li> <li><a href='#ZFP'>Zinc Finger Print alignment</a></li> </ul> ------ <h2 id='General'>General</h2> | | | |--|--| | <b>Gene ensembl <br><i>Link to the corresponding Ensembl site</i></b> | <a href="http://www.ensembl.org/Multi/Search/Results?q=ENSG00000144792;site=ensembl~">ENSG00000144792</a> | | <b>Age (years) <br><i>Estimated age of the KRAB-ZNF as in <a href="https://pubmed.ncbi.nlm.nih.gov/28273063/">Imbeault et al</a></i></b> | 105 | | <b>Age (species) <br><i>The name of the species where the KRAB-ZNF was first observed as in <a href="https://pubmed.ncbi.nlm.nih.gov/28273063/">Imbeault et al</a></i></b> | Cape golden mole | | <b>\#peaks in exo <br><i>Number of peaks found in the ChIP-exo dataset</i></b> | | | <b>Incomplete KRAB domain</b> | | | <b>Interacts with K1</b> | Not in database | | <b>Interacts with</b> | Not in database | | <b>ORF sequence</b> | | | <b>Zinc fingers</b> | 10 | <div class="adroite"><a href="#"><b>back to top</b></a></div> ------ <h2 id='Polymorphism'>Polymorphism</h2> <table> <tr><th>gnomAD genome</th><th>gnomAD exome</th></tr> <tr><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 114.844 | | Exon (no domain, nor Zfinger) | 114.844 | | Krab domain | NA | | Zinc finger | 101.449 | | Region | #miss.SNP | |--|--| | Zinc finger | 50 | | C2H2 | 2 | | Zinc finger print | 0 | <input type="button" id="button" style="float:left" value="[+] Help" onclick="afficher()" /><br> <form id="doc" style="display: none;"> <br>Gene view with all variants found at the gene of interest (canonical transcript).<br><ul><li> blue dots: synonymous & noncoding variants.</li><li> red dots: missense variants.</li><li> orange dots: splice variants.</li><li> green dots: Loss of function variants (frameshift, stop_lost or stop_gained mutation).</li><li> GERP score: a conservation score widely used to look at constraint across genes and non-coding regions, and also used in the best pathogenic variant scoring softwares. A score above 2 is considered conserved.</li><li> Green boxes on the genes: the exons.</li><li> Red boxes: the KRAB domain.</li><li> Blue boxes: the zinc finger domains.</li><li> Pink boxes: degenerate zinc finger domains.</li></ul> </form><br> <a href='../MAF_gnomAD/ZNF660.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZNF660.png" width="400" height="200" /> </a> <input type="button" id="button_2" style="float:left" value="[+] Help" onclick="afficher_2()" /><br> <form id="doc_2" style="display: none;"> <br>Zoomed plot of variants in each zinc finger domain with the specific amino acids plotted.<ul><li>blue dots: synonymous & noncoding variants.</li><li>red dots: missense variants.</li><li>orange dots: splice variants.</li><li>green dots: Loss of function variants (frameshift, stop_lost or stop_gained mutation).</li><li> Blue boxes: The positions of the DNA contacting amino acids</li><li> Red boxes: The Cytidine and Histidine amino acid positions</li></ul> </form><br> <a href='../Zfinger_gnomAD/ZNF660.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZNF660.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 90.504 | | Exon (no domain, nor Zfinger) | 90.504 | | Krab domain | NA | | Zinc finger | 478.261 | | Region | #miss.SNP | |--|--| | Zinc finger | 232 | | C2H2 | 4 | | Zinc finger print | 0 | <input type="button" id="button1" style="float:left" value="[+] Help" onclick="afficher1()" /><br> <form id="doc1" style="display: none;"> <br>Gene view with all variants found at the gene of interest (canonical transcript).<br><ul><li> blue dots: synonymous & noncoding variants.</li><li> red dots: missense variants.</li><li> orange dots: splice variants.</li><li> green dots: Loss of function variants (frameshift, stop_lost or stop_gained mutation).</li><li> GERP score: a conservation score widely used to look at constraint across genes and non-coding regions, and also used in the best pathogenic variant scoring softwares. A score above 2 is considered conserved.</li><li> Green boxes on the genes: the exons.</li><li> Red boxes: the KRAB domain.</li><li> Blue boxes: the zinc finger domains.</li><li> Pink boxes: degenerate zinc finger domains.</li></ul> </form><br> <a href='../MAF_gnomAD_exome/ZNF660.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZNF660.png" width="400" height="200" /> </a> <input type="button" id="button2" style="float:left" value="[+] Help" onclick="afficher2()" /><br> <form id="doc2" style="display: none;"> <br>Zoomed plot of variants in each zinc finger domain with the specific amino acids plotted.<ul><li>blue dots: synonymous & noncoding variants.</li><li>red dots: missense variants.</li><li>orange dots: splice variants.</li><li>green dots: Loss of function variants (frameshift, stop_lost or stop_gained mutation).</li><li> Blue boxes: The positions of the DNA contacting amino acids</li><li> Red boxes: The Cytidine and Histidine amino acid positions</li></ul> </form><br> <a href='../Zfinger_gnomAD_exome/ZNF660.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZNF660.png" width="400" height="200" /> </a> </td></tr> </table> <div class="adroite"><a href="#"><b>back to top</b></a></div> ------ <h2 id='Expression in tissues (from GTEx)'>Expression in tissues (from GTEx)</h2> <input type="button" id="GTX_button" style="float:left" value="Open Expression Information from GTEx Website" onclick="document.location.href='https://www.gtexportal.org/home/gene/ZNF660'" /><br><br> <div class="adroite"><a href="#"><b>back to top</b></a></div> ------ <h2 id='CisBP motifs'>CisBP motifs</h2> <input type="button" id="CisBP_button" style="float:left" value="Open CisBP Website" onclick="document.location.href='http://cisbp.ccbr.utoronto.ca'" /><br><br> <table> <tr><th>Forward</th><th>Reverse</th></tr> <tr><td> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000144792 </td></tr><tr><th> Motif_ID </th><td> M04479_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZNF660_FL_HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04479_2.00_fwd.png"><img src="../logos_kzfp/M04479_2.00_fwd.png" width="200" height="100"></td> <td><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><a href="../logos_kzfp/M04479_2.00_rev.png"><img src="../logos_kzfp/M04479_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000144792 </td></tr><tr><th> Motif_ID </th><td> M04480_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZNF660_FL_Methyl-HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04480_2.00_fwd.png"><img src="../logos_kzfp/M04480_2.00_fwd.png" width="200" height="100"></td> <td><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><a href="../logos_kzfp/M04480_2.00_rev.png"><img src="../logos_kzfp/M04480_2.00_rev.png" width="200" height="100"></td></tr> </td></tr> </table> <div class="adroite"><a href="#"><b>back to top</b></a></div> ------ <h2 id="ZFP">ZFP alignment</h2> <input type="button" id="button_zfp" style="float:left" value="[+] Help" onclick="afficher_zfp()"/><br> <form id="doc_zfp" style="display: none;"> <br>Zinc Finger Print alignment of the ZFP of interest against all other ZFPs </form> <a href="../ZFP_CAZF_score/ZNF660.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZNF660.png" width="400" height="200" /> </a> <table> <tr> <td></td> <td>GeneName1</td> <td>KZFP1</td> <td>GeneName2</td> <td>KZFP2</td> <td>CAZF_score</td> </tr> <tr> <td>143152</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF251</td> <td>NC_000008.10_RF_OOFZFA_778</td> <td>0.143273542600897</td> </tr> <tr> <td>143599</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF790</td> <td>NC_000019.9_RF_OOFZFA_415</td> <td>0.137892376681614</td> </tr> <tr> <td>143111</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZSCAN21</td> <td>NC_000007.13_FF_OOFZFA_269</td> <td>0.130452507134121</td> </tr> <tr> <td>143845</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>KRBOX4</td> <td>NC_000023.10_FF_OOFZFA_126</td> <td>0.124088516279977</td> </tr> <tr> <td>142897</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF852</td> <td>NC_000003.11_RF_OOFZFA_563</td> <td>0.115226253567061</td> </tr> <tr> <td>142898</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZKSCAN7</td> <td>NC_000003.11_FF_OOFZFA_103</td> <td>0.115226253567061</td> </tr> <tr> <td>143157</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>0.112090375991721</td> </tr> <tr> <td>143566</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF675</td> <td>NC_000019.9_RF_OOFZFA_381</td> <td>0.109616342800199</td> </tr> <tr> <td>143605</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF420</td> <td>NC_000019.9_FF_OOFZFA_129</td> <td>0.102756528620417</td> </tr> <tr> <td>142900</td> <td>ZNF660</td> <td>NC_000003.11_FF_OOFZFA_104</td> <td>ZNF35</td> <td>NC_000003.11_FF_OOFZFA_106</td> <td>0.101644245142003</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZNF660.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>