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=ENSG00000170631;site=ensembl~">ENSG00000170631</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> | 97.5 | | <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> | Minke whale | | <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> | 15 | <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 | 65.367 | | Exon (no domain, nor Zfinger) | 65.367 | | Krab domain | NA | | Zinc finger | 67.633 | | Region | #miss.SNP | |--|--| | Zinc finger | 44 | | C2H2 | 2 | | Zinc finger print | 7 | <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/ZNF16.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZNF16.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/ZNF16.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZNF16.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 204.511 | | Exon (no domain, nor Zfinger) | 204.511 | | Krab domain | NA | | Zinc finger | 271.498 | | Region | #miss.SNP | |--|--| | Zinc finger | 196 | | C2H2 | 27 | | Zinc finger print | 26 | <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/ZNF16.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZNF16.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/ZNF16.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZNF16.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/ZNF16'" /><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> ENSG00000170631 </td></tr><tr><th> Motif_ID </th><td> M08251_2.00 </td></tr><tr><th> Motif_Type </th><td> ChIP-seq </td></tr><tr><th> MSource_Identifier </th><td> Najafabadi2015b </td></tr><tr><th> Study_ID </th><td> ZNF16 </td></tr><tr><th> Author_Year </th><td> Najafabadi_2015b </td></tr><tr><th> PMID </th><td> 25690854 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M08251_2.00_fwd.png"><img src="../logos_kzfp/M08251_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/M08251_2.00_rev.png"><img src="../logos_kzfp/M08251_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000170631 </td></tr><tr><th> Motif_ID </th><td> M08336_2.00 </td></tr><tr><th> Motif_Type </th><td> ChIP-seq </td></tr><tr><th> MSource_Identifier </th><td> Schmitges2016 </td></tr><tr><th> Study_ID </th><td> P17020_7-12.RCADE </td></tr><tr><th> Author_Year </th><td> Schmitges_2016 </td></tr><tr><th> PMID </th><td> 27852650 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M08336_2.00_fwd.png"><img src="../logos_kzfp/M08336_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/M08336_2.00_rev.png"><img src="../logos_kzfp/M08336_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/ZNF16.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZNF16.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>456975</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF792</td> <td>NC_000019.9_RF_OOFZFA_405</td> <td>0.225448636427865</td> </tr> <tr> <td>456226</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF678</td> <td>NC_000001.10_FF_OOFZFA_479</td> <td>0.218133899471157</td> </tr> <tr> <td>457129</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF419</td> <td>NC_000019.9_FF_OOFZFA_241</td> <td>0.202840186519712</td> </tr> <tr> <td>457067</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF83</td> <td>NC_000019.9_RF_OOFZFA_471</td> <td>0.196243545820332</td> </tr> <tr> <td>456548</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF252P</td> <td>NC_000008.10_RF_OOFZFA_782</td> <td>0.193318550885316</td> </tr> <tr> <td>457166</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF324B</td> <td>NC_000019.9_FF_OOFZFA_266</td> <td>0.190122933446376</td> </tr> <tr> <td>457167</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF324</td> <td>NC_000019.9_FF_OOFZFA_267</td> <td>0.187425334309607</td> </tr> <tr> <td>456940</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF257</td> <td>NC_000019.9_FF_OOFZFA_73</td> <td>0.186475269728835</td> </tr> <tr> <td>456932</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF708</td> <td>NC_000019.9_RF_OOFZFA_357</td> <td>0.186028047449948</td> </tr> <tr> <td>456546</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>ZNF7</td> <td>NC_000008.10_FF_OOFZFA_378</td> <td>0.183799053502804</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZNF16.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>