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=ENSG00000180532;site=ensembl~">ENSG00000180532</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> | Cape golden mole | | <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 | 59.216 | | Exon (no domain, nor Zfinger) | 59.216 | | Krab domain | 71.73 | | Zinc finger | 76.087 | | Region | #miss.SNP | |--|--| | Zinc finger | 14 | | C2H2 | 0 | | Zinc finger print | 1 | <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/ZSCAN4.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZSCAN4.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/ZSCAN4.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZSCAN4.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 144.256 | | Exon (no domain, nor Zfinger) | 144.256 | | Krab domain | 210.97 | | Zinc finger | 224.638 | | Region | #miss.SNP | |--|--| | Zinc finger | 42 | | C2H2 | 6 | | Zinc finger print | 6 | <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/ZSCAN4.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZSCAN4.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/ZSCAN4.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZSCAN4.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/ZSCAN4'" /><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> ENSG00000180532 </td></tr><tr><th> Motif_ID </th><td> M02919_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> ZSCAN4_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/M02919_2.00_fwd.png"><img src="../logos_kzfp/M02919_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/M02919_2.00_rev.png"><img src="../logos_kzfp/M02919_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000180532 </td></tr><tr><th> Motif_ID </th><td> M04593_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> ZSCAN4_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/M04593_2.00_fwd.png"><img src="../logos_kzfp/M04593_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/M04593_2.00_rev.png"><img src="../logos_kzfp/M04593_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000180532 </td></tr><tr><th> Motif_ID </th><td> M04594_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> ZSCAN4_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/M04594_2.00_fwd.png"><img src="../logos_kzfp/M04594_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/M04594_2.00_rev.png"><img src="../logos_kzfp/M04594_2.00_rev.png" width="200" height="100"></td></tr> <tr><td><table><tr><th> ENSEMBL ID </th><td> ENSG00000180532 </td></tr><tr><th> Motif_ID </th><td> M05852_2.00 </td></tr><tr><th> Motif_Type </th><td> SMiLE-seq </td></tr><tr><th> MSource_Identifier </th><td> Isakova2017 </td></tr><tr><th> Study_ID </th><td> ZSCAN4 </td></tr><tr><th> Author_Year </th><td> Isakova_2017 </td></tr><tr><th> PMID </th><td> 28092692 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M05852_2.00_fwd.png"><img src="../logos_kzfp/M05852_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/M05852_2.00_rev.png"><img src="../logos_kzfp/M05852_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/ZSCAN4.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZSCAN4.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>1171484</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF300P1</td> <td>NC_000005.9_RF_OOFZFA_855</td> <td>0.163617886178862</td> </tr> <tr> <td>1172148</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF285B</td> <td>NC_000019.9_FF_OOFZFA_168</td> <td>0.13719512195122</td> </tr> <tr> <td>1171458</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF969P</td> <td>NC_000004.11_FF_OOFZFA_253</td> <td>0.125</td> </tr> <tr> <td>1172269</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF8</td> <td>NC_000019.9_FF_OOFZFA_262</td> <td>0.120967741935484</td> </tr> <tr> <td>1172367</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF75D</td> <td>NC_000023.10_RF_OOFZFA_710</td> <td>0.115079365079365</td> </tr> <tr> <td>1172481</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF75D</td> <td>NW_004070887.1_RF_OOFZFA_7</td> <td>0.115079365079365</td> </tr> <tr> <td>1172345</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>KRBOX4</td> <td>NC_000023.10_FF_OOFZFA_126</td> <td>0.109375</td> </tr> <tr> <td>1172254</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF552</td> <td>NC_000019.9_RF_OOFZFA_519</td> <td>0.105769230769231</td> </tr> <tr> <td>1171615</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF705G</td> <td>NC_000008.10_RF_OOFZFA_403</td> <td>0.0882352941176471</td> </tr> <tr> <td>1171839</td> <td>ZSCAN4</td> <td>NC_000019.9_FF_OOFZFA_248</td> <td>ZNF75A</td> <td>NC_000016.9_FF_OOFZFA_11</td> <td>0.0873015873015873</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZSCAN4.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>