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=ENSG00000197037;site=ensembl~">ENSG00000197037</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> | Hoffmann's two-toed sloth | | <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> | 7 | <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 | 75.42 | | Exon (no domain, nor Zfinger) | 75.42 | | Krab domain | 84.388 | | Zinc finger | 74.534 | | Region | #miss.SNP | |--|--| | Zinc finger | 21 | | C2H2 | 1 | | Zinc finger print | 2 | <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/ZSCAN25.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZSCAN25.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/ZSCAN25.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZSCAN25.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 96.114 | | Exon (no domain, nor Zfinger) | 96.114 | | Krab domain | 210.97 | | Zinc finger | 248.447 | | Region | #miss.SNP | |--|--| | Zinc finger | 73 | | C2H2 | 6 | | Zinc finger print | 8 | <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/ZSCAN25.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZSCAN25.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/ZSCAN25.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZSCAN25.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/ZSCAN25'" /><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/ZSCAN25.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZSCAN25.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>373280</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZKSCAN2</td> <td>NC_000016.9_RF_OOFZFA_279</td> <td>0.110714285714286</td> </tr> <tr> <td>373054</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF517</td> <td>NC_000008.10_FF_OOFZFA_377</td> <td>0.105311355311355</td> </tr> <tr> <td>372985</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF394</td> <td>NC_000007.13_RF_OOFZFA_632</td> <td>0.1</td> </tr> <tr> <td>373513</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF793</td> <td>NC_000019.9_FF_OOFZFA_134</td> <td>0.1</td> </tr> <tr> <td>373162</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF641</td> <td>NC_000012.11_RF_OOFZFA_440</td> <td>0.0994285714285714</td> </tr> <tr> <td>373599</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF761</td> <td>NC_000019.9_FF_OOFZFA_207</td> <td>0.0977795612627073</td> </tr> <tr> <td>372980</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF273</td> <td>NC_000007.13_FF_OOFZFA_176</td> <td>0.0911255411255411</td> </tr> <tr> <td>373224</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZSCAN29</td> <td>NC_000015.9_RF_OOFZFA_259</td> <td>0.0857142857142857</td> </tr> <tr> <td>373249</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZNF263</td> <td>NC_000016.9_FF_OOFZFA_10</td> <td>0.0835164835164835</td> </tr> <tr> <td>373239</td> <td>ZSCAN25</td> <td>NC_000007.13_FF_OOFZFA_266</td> <td>ZSCAN32</td> <td>NC_000016.9_RF_OOFZFA_236</td> <td>0.0785714285714286</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZSCAN25.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>