Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes-supplmentary files
Creators: name: Armijos-Jaramillo Vinicio
Publisher: name: Zenodo
Year: 2022

description: Figure and Fig captures <strong><em>Table S1</em></strong>. <strong>Genomic locations of <em>de novo</em> predicted ERVs in humans.</strong> <strong><em>Table S2.</em></strong> <strong>Summary of RetroTector analysis and alignments between </strong><strong><em>INPP5B</em></strong><strong> orthologous vs ERV region in the human gene</strong>. The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S3. </em></strong><strong>Summary of RetroTector analysis and alignments between </strong><strong><em>DET1</em></strong><strong> orthologous vs ERV region in the human gene.</strong> The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S4.</em></strong> <strong>Summary of RetroTector analysis and alignments between <em>PSMA1</em> orthologous vs ERV region in the human gene.</strong> The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S5. </em></strong><strong>Summary of RetroTector analysis and alignments between </strong><strong><em>USH2A</em></strong><strong> orthologous vs ERV region in the human gene.</strong> The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S6. </em></strong><strong>Summary of RetroTector analysis and alignments between </strong><strong><em>MACROD2</em></strong><strong> orthologous vs ERV1 region in the human gene.</strong> The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S7.</em></strong><strong> Summary of RetroTector analysis and alignments between </strong><strong><em>MACROD2</em></strong><strong> orthologous vs ERV2 region in the human gene.</strong> The species found in the table correspond to primates; the species underlined in purple are those that were detected in RetroTector and BLASTN. <strong><em>Table S8. </em></strong><strong>Summary of RetroTector analysis and alignments between </strong><strong><em>INPP5B</em></strong><strong> paralogous vs ERV region in the human gene. </strong>Only one positive result in RetroTector was found in <em>SYNJ1</em>; however, according to the alignment result, it is not the same retroviral sequence. Therefore, it is a different ERV than the one found in the <em>INPP5B</em> gene. <strong><em>Table S9. </em></strong><strong>Summary of RetroTector analysis and alignments between </strong><strong><em>USH2A</em></strong><strong> paralogous vs ERV region in the human gene. </strong>Only two positive results in RetroTector were found in <em>LAMA2</em> and <em>NTN4</em>; however, according to the alignment result, it is not the same retroviral sequence. Therefore, it is a different ERV than the one found in the <em>USH2A</em> gene. <strong><em>Table S10.</em></strong> Transcription factors (TF) associated exclusively with ERVs, excluding all TFs shared by orthologs and paralogs annotated in equivalent structural sections. <strong><em>Fig S1.</em></strong> Mammal species tree with the location of the minimum common ancestor where the retroviral infection occurred for the genes analyzed in this work. <strong><em>Fig S2.</em></strong> Mammal species tree with the location of the minimum common ancestor where the retrovirus infection occurred for the <em>INPP5B</em> gene. Light blue represents the species where ERVs were detected with both RetroTector and BLASTN, purple the species detected only by alignment with BLASTN, and pink the species detected by RetroTector. <strong><em>Fig S3.</em></strong> Mammal species tree with the location of the minimum common ancestor where the retrovirus infection occurred for the <em>DET1</em> gene. Light blue represents the species where ERVs were detected with both RetroTector and BLASTN, purple the species detected only by alignment with BLASTN, and pink the species detected by RetroTector. <strong><em>Fig S4.</em></strong> Mammal species tree with the location of the minimum common ancestor where the retrovirus infection occurred for the <em>PSMA1 </em>gene. Light blue represents the species where ERVs were detected with both RetroTector and BLASTN, purple the species detected only by alignment with BLASTN, and pink the species detected by RetroTector. <strong><em>Fig S5.</em></strong> Mammal species tree with the location of the minimum common ancestor where the retrovirus infection occurred for the <em>USH2A</em> gene. Light blue represents the species where ERVs were detected with both RetroTector and BLASTN, purple the species detected only by alignment with BLASTN, and pink the species detected by RetroTector <strong><em>Fig S6. </em></strong>Mammal species tree with the location of the minimum common ancestor where the retrovirus infection occurred for the <em>MACROD2</em> gene. Light blue represents the species where ERVs were detected with both RetroTector and BLASTN, purple the species detected only by alignment with BLASTN, and pink the species detected by RetroTector. <strong><em>Fig S7.</em></strong> <em>INPP5B</em> ERV expression in several tissues. Data visualized in UCSC genome browser (http://genome.ucsc.edu) using the GTEx portal data (https://gtexportal.org/).