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='#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=ENSG00000174586;site=ensembl~">ENSG00000174586</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> | 163.7 | | <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> | Gray short-tailed opossum | | <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> | 14 | <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 | 83.622 | | Exon (no domain, nor Zfinger) | 83.622 | | Krab domain | NA | | Zinc finger | 104.555 | | Region | #miss.SNP | |--|--| | Zinc finger | 64 | | C2H2 | 5 | | 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/ZNF497.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZNF497.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/ZNF497.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZNF497.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 108.997 | | Exon (no domain, nor Zfinger) | 108.997 | | Krab domain | NA | | Zinc finger | 238.095 | | Region | #miss.SNP | |--|--| | Zinc finger | 151 | | C2H2 | 8 | | 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/ZNF497.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZNF497.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/ZNF497.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZNF497.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/ZNF497'" /><br><br> <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/ZNF497.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZNF497.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>1201313</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF837</td> <td>NC_000019.9_RF_OOFZFA_530</td> <td>0.205584169151532</td> </tr> <tr> <td>1200617</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF680</td> <td>NC_000007.13_RF_OOFZFA_560</td> <td>0.136525644740655</td> </tr> <tr> <td>1201101</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF730</td> <td>NC_000019.9_FF_OOFZFA_83</td> <td>0.128006374963779</td> </tr> <tr> <td>1201110</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF726</td> <td>NC_000019.9_FF_OOFZFA_86</td> <td>0.125553857906799</td> </tr> <tr> <td>1201089</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF43</td> <td>NC_000019.9_RF_OOFZFA_361</td> <td>0.121117335823218</td> </tr> <tr> <td>1201235</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF677</td> <td>NC_000019.9_RF_OOFZFA_489</td> <td>0.120812324929972</td> </tr> <tr> <td>1201086</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF429</td> <td>NC_000019.9_FF_OOFZFA_69</td> <td>0.119417275106764</td> </tr> <tr> <td>1200618</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF107</td> <td>NC_000007.13_FF_OOFZFA_173</td> <td>0.116819455054749</td> </tr> <tr> <td>1201108</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF681</td> <td>NC_000019.9_RF_OOFZFA_382</td> <td>0.113879789203817</td> </tr> <tr> <td>1201078</td> <td>ZNF497</td> <td>NC_000019.9_RF_OOFZFA_529</td> <td>ZNF85</td> <td>NC_000019.9_FF_OOFZFA_61</td> <td>0.110703953712633</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZNF497.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>