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=ENSG00000140265;site=ensembl~">ENSG00000140265</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> | 179.2 | | <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> | Platypus | | <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> | 6 | <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 | 64.343 | | Exon (no domain, nor Zfinger) | 64.343 | | Krab domain | 65.041 | | Zinc finger | 74.879 | | Region | #miss.SNP | |--|--| | Zinc finger | 23 | | C2H2 | 7 | | Zinc finger print | 4 | <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/ZSCAN29.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZSCAN29.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/ZSCAN29.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZSCAN29.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 115.103 | | Exon (no domain, nor Zfinger) | 115.103 | | Krab domain | 174.797 | | Zinc finger | 253.623 | | Region | #miss.SNP | |--|--| | Zinc finger | 78 | | C2H2 | 11 | | Zinc finger print | 12 | <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/ZSCAN29.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZSCAN29.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/ZSCAN29.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZSCAN29.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/ZSCAN29'" /><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/ZSCAN29.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZSCAN29.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>658803</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF500</td> <td>NC_000016.9_RF_OOFZFA_242</td> <td>0.543129770992366</td> </tr> <tr> <td>658840</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZKSCAN2</td> <td>NC_000016.9_RF_OOFZFA_279</td> <td>0.487277353689567</td> </tr> <tr> <td>658799</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZSCAN32</td> <td>NC_000016.9_RF_OOFZFA_236</td> <td>0.400127226463104</td> </tr> <tr> <td>658742</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF891</td> <td>NC_000012.11_RF_OOFZFA_637</td> <td>0.171777660787927</td> </tr> <tr> <td>658444</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF300P1</td> <td>NC_000005.9_RF_OOFZFA_855</td> <td>0.170238794284596</td> </tr> <tr> <td>659142</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF468</td> <td>NC_000019.9_RF_OOFZFA_476</td> <td>0.151187446988974</td> </tr> <tr> <td>658443</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF300</td> <td>NC_000005.9_RF_OOFZFA_854</td> <td>0.14440203562341</td> </tr> <tr> <td>658639</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF484</td> <td>NC_000009.11_RF_OOFZFA_496</td> <td>0.14440203562341</td> </tr> <tr> <td>659308</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF41</td> <td>NC_000023.10_RF_OOFZFA_503</td> <td>0.129714626211872</td> </tr> <tr> <td>658811</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>ZNF764</td> <td>NC_000016.9_RF_OOFZFA_292</td> <td>0.126349039220848</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZSCAN29.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>