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='#Genomic regions'>Genomic regions</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=ENSG00000196152;site=ensembl~">ENSG00000196152</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> | Gray short-tailed opossum | | <b>\#peaks in exo <br><i>Number of peaks found in the ChIP-exo dataset</i></b> | 403 | | <b>Incomplete KRAB domain</b> | | | <b>Interacts with K1</b> | YES , FC=2.7 , FDR=0.00388 | | <b>Interacts with</b> | IPO8, HSPA4L, GLA, EIF3E, TIMM50, USP9X, DNAJA3, TSEN34, GOPC, STUB1, PPP2R1A, EIF3D, HSPH1, BAG2, RPS15, DNAJA2, DDB1, TCAF1, PSMA3, EIF3A, CCAR2, HSPA4, DNAJA1, HSPA8, EFTUD2, STIP1 | | <b>ORF sequence</b> | <a href="../ORFseq/ZNF79.txt">Open</a> | | <b>Zinc fingers</b> | 11 | <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 | 73.147 | | Exon (no domain, nor Zfinger) | 73.147 | | Krab domain | 74.972 | | Zinc finger | 65.876 | | Region | #miss.SNP | |--|--| | Zinc finger | 30 | | C2H2 | 3 | | Zinc finger print | 6 | <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/ZNF79.pdf'> <img src="../MAF_gnomAD/MAF_gnomAD/ZNF79.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/ZNF79.pdf'> <img src="../Zfinger_gnomAD/Zfinger_gnomAD/ZNF79.png" width="400" height="200" /> </a> </td><td><table></table> | Region | #miss.SNP x Kb | |--|--| | Exon | 206.93 | | Exon (no domain, nor Zfinger) | 206.93 | | Krab domain | 85.998 | | Zinc finger | 247.694 | | Region | #miss.SNP | |--|--| | Zinc finger | 129 | | C2H2 | 26 | | Zinc finger print | 20 | <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/ZNF79.pdf'> <img src="../MAF_gnomAD_exome/MAF_gnomAD_exome/ZNF79.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/ZNF79.pdf'> <img src="../Zfinger_gnomAD_exome/Zfinger_gnomAD_exome/ZNF79.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/ZNF79'" /><br><br> <a href="../GTEx_cecile/Figures_transcripts/Histogram_coding/Histogram_ZNF79.png"><img src="../GTEx_cecile/Figures_transcripts/Histogram_coding/Histogram_ZNF79.png" height="400" width="400" /></a> <a href="../GTEx_cecile/Figures_transcripts/Heatmap_coding/Heatmap_C_ZNF79.png"><img src="../GTEx_cecile/Figures_transcripts/Heatmap_coding/Heatmap_C_ZNF79.png" height="400" width="400" /></a><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> ENSG00000196152 </td></tr><tr><th> Motif_ID </th><td> M07697_2.00 </td></tr><tr><th> Motif_Type </th><td> ChIP-seq+ChIP-exo </td></tr><tr><th> MSource_Identifier </th><td> Barazandeh2018 </td></tr><tr><th> Study_ID </th><td> ZNF79.RCADE.ReprocessedData </td></tr><tr><th> Author_Year </th><td> Barazandeh_2018 </td></tr><tr><th> PMID </th><td> 29146583 </td></tr><tr><th> TF_Status </th><td> D </td></tr></table><a href="../logos_kzfp/M07697_2.00_fwd.png"><img src="../logos_kzfp/M07697_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/M07697_2.00_rev.png"><img src="../logos_kzfp/M07697_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='Genomic regions'>Genomic regions</h2> <a href='../figs/ZNF79.pdf'> <img src="../figs/figs/ZNF79.png" width="400" height="400" /><br><br> </a> <input type="button" id="GenReg_button" style="float:left" value="Open Table with Annotation for Each Bound Loci" onclick="document.location.href='../tables/ZNF79_overlaps.xls'" /><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/ZNF79.pdf"> <img src="../ZFP_CAZF_score/pngs/plotzfp_ZNF79.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>505540</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF154</td> <td>NC_000019.9_RF_OOFZFA_516</td> <td>0.196082337317397</td> </tr> <tr> <td>505530</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF773</td> <td>NC_000019.9_FF_OOFZFA_242</td> <td>0.179568681794561</td> </tr> <tr> <td>505539</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF551</td> <td>NC_000019.9_FF_OOFZFA_249</td> <td>0.177760145857249</td> </tr> <tr> <td>505192</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF286B</td> <td>NC_000017.10_RF_OOFZFA_220</td> <td>0.171403275785746</td> </tr> <tr> <td>505537</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF211</td> <td>NC_000019.9_FF_OOFZFA_247</td> <td>0.169521912350598</td> </tr> <tr> <td>505189</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF286A</td> <td>NC_000017.10_FF_OOFZFA_28</td> <td>0.159716688800354</td> </tr> <tr> <td>505162</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZFP90</td> <td>NC_000016.9_FF_OOFZFA_151</td> <td>0.158750184447396</td> </tr> <tr> <td>504948</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF16</td> <td>NC_000008.10_RF_OOFZFA_781</td> <td>0.152714143426295</td> </tr> <tr> <td>505375</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF792</td> <td>NC_000019.9_RF_OOFZFA_405</td> <td>0.152044881697699</td> </tr> <tr> <td>504783</td> <td>ZNF79</td> <td>NC_000009.11_FF_OOFZFA_284</td> <td>ZNF879</td> <td>NC_000005.9_FF_OOFZFA_472</td> <td>0.147712181576723</td> </tr> </table> <input type="button" id="button_csv" style="float:left" value="Open full table" onclick="document.location.href='../ZFP_CAZF_score/csv/ZNF79.xlsx'" /><br> <div class="adroite"><a href="#"><b>back to top</b></a></div>