KRABopedia - The place to find Krab Zinc Finger information

<u>Section list:</u> <ul> <li><a href='#General'>General</a></li> <li><a href='#Age'>Cross-Species Sequence Comparison</a></li> <li><a href='#Polymorphism'>Polymorphism</a></li> <li><a href='#Expression in tissues (from GTEx)'>Expression in tissues (from GTEx)</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=ENSG00000214189;site=ensembl~">ENSG00000214189</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> | 43.1 | | <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> | Nancy Ma's night monkey | | <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> | 1 | <div class="adroite"><a href="#"><b>back to top</b></a></div> ------ <h2 id='Age'>Cross-Species Sequence Comparison</h2> <input type="button" id="button_age" style="float:left" value="[+] Help" onclick="afficher_age()" /><br> <form id="doc_age" style="display: none;"> The 4 amino acids known to bind DNA were extracted from Zinc Finger protein sequence (positions -1, 2, 3, 6). Based on this subset of amino acids, we aligned the human Zinc Finger to every other Zinc Fingers in human and 68 foreign species. In the plot X.X, the alignment scores between the Zinc Finger of interest and other Zinc Fingers was drawn as one boxplot for each species. The yellow line joins the dots corresponding to the best alignment scores found for each species. Same was done for the KRAB domain, but only showing the best alignments joined by a red line. A dashed vertical red line shows the age estimate from Imbeault et al. 2018. </form><br> <a href='../EvolLine/EvoLine_ZNF788.pdf'> <img src="../EvolLine/EvolLine/EvoLine_ZNF788.png" height="400" width="400" /> </a> <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 | 130.058 | | Exon (no domain, nor Zfinger) | 130.058 | | Krab domain | 148.707 | | Zinc finger | NA | | Region | #miss.SNP | |--|--| | Zinc finger | NA | | C2H2 | NA | | Zinc finger print | NA | <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/ZNF788.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZNF788.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/ZNF788.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZNF788.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 216.763 | | Exon (no domain, nor Zfinger) | 216.763 | | Krab domain | 62.5 | | Zinc finger | NA | | Region | #miss.SNP | |--|--| | Zinc finger | NA | | C2H2 | NA | | Zinc finger print | NA | <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/ZNF788.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZNF788.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/ZNF788.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZNF788.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/ZNF788'" /><br><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>