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=ENSG00000196812;site=ensembl~">ENSG00000196812</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> | Tammar wallaby | | <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> | 4 | <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 | 48.946 | | Exon (no domain, nor Zfinger) | 48.946 | | Krab domain | 40.161 | | Zinc finger | 61.594 | | Region | #miss.SNP | |--|--| | Zinc finger | 13 | | C2H2 | 1 | | 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/ZSCAN16.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZSCAN16.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/ZSCAN16.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZSCAN16.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 158.133 | | Exon (no domain, nor Zfinger) | 158.133 | | Krab domain | 204.819 | | Zinc finger | 221.014 | | Region | #miss.SNP | |--|--| | Zinc finger | 43 | | C2H2 | 7 | | 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/ZSCAN16.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZSCAN16.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/ZSCAN16.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZSCAN16.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/ZSCAN16'" /><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> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M02924_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Jolma2013 </td></tr><tr><th> Study_ID </th><td> ZNF435_1 </td></tr><tr><th> Author_Year </th><td> Jolma_2013 </td></tr><tr><th> PMID </th><td> 23332764 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M02924_2.00_fwd.png"><img src="../logos_kzfp/M02924_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/M02924_2.00_rev.png"><img src="../logos_kzfp/M02924_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M04623_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZSCAN16_eDBD_HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04623_2.00_fwd.png"><img src="../logos_kzfp/M04623_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/M04623_2.00_rev.png"><img src="../logos_kzfp/M04623_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M04624_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZSCAN16_eDBD_Methyl-HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04624_2.00_fwd.png"><img src="../logos_kzfp/M04624_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/M04624_2.00_rev.png"><img src="../logos_kzfp/M04624_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M04625_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZSCAN16_FL_HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04625_2.00_fwd.png"><img src="../logos_kzfp/M04625_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/M04625_2.00_rev.png"><img src="../logos_kzfp/M04625_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M04626_2.00 </td></tr><tr><th> Motif_Type </th><td> SELEX </td></tr><tr><th> MSource_Identifier </th><td> Yin2017 </td></tr><tr><th> Study_ID </th><td> ZSCAN16_FL_Methyl-HT-SELEX </td></tr><tr><th> Author_Year </th><td> Yin_2017 </td></tr><tr><th> PMID </th><td> 28473536 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M04626_2.00_fwd.png"><img src="../logos_kzfp/M04626_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/M04626_2.00_rev.png"><img src="../logos_kzfp/M04626_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000196812 </td></tr><tr><th> Motif_ID </th><td> M08377_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> Q9H4T2.MEME </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/M08377_2.00_fwd.png"><img src="../logos_kzfp/M08377_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/M08377_2.00_rev.png"><img src="../logos_kzfp/M08377_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/ZSCAN16.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZSCAN16.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>276109</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZKSCAN8</td> <td>NC_000006.11_FF_OOFZFA_79</td> <td>0.21195652173913</td> </tr> <tr> <td>276794</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF677</td> <td>NC_000019.9_RF_OOFZFA_489</td> <td>0.200614366729679</td> </tr> <tr> <td>276867</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF274</td> <td>NC_000019.9_FF_OOFZFA_259</td> <td>0.170548654244306</td> </tr> <tr> <td>276084</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF300P1</td> <td>NC_000005.9_RF_OOFZFA_855</td> <td>0.163176033934252</td> </tr> <tr> <td>276083</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF300</td> <td>NC_000005.9_RF_OOFZFA_854</td> <td>0.154503105590062</td> </tr> <tr> <td>276950</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF630</td> <td>NC_000023.10_RF_OOFZFA_509</td> <td>0.153985507246377</td> </tr> <tr> <td>277075</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF630</td> <td>NW_004070880.2_RF_OOFZFA_7</td> <td>0.153985507246377</td> </tr> <tr> <td>276765</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF836</td> <td>NC_000019.9_RF_OOFZFA_469</td> <td>0.15123688155922</td> </tr> <tr> <td>276746</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF229</td> <td>NC_000019.9_RF_OOFZFA_444</td> <td>0.150171624713959</td> </tr> <tr> <td>276764</td> <td>ZSCAN16</td> <td>NC_000006.11_FF_OOFZFA_78</td> <td>ZNF616</td> <td>NC_000019.9_RF_OOFZFA_467</td> <td>0.141358157554886</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZSCAN16.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>