Harlequin
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000017 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 6896 |
| Kimura value | 6.23 |
| Tau index | 0.9729 |
| Description | Internal region of ERV1 endogenous retrovirus, Harlequin subfamily |
| Comment | Harlequin is an internal part of an endogenous retrovirus-like element flanked by LTR2s. Its consensus sequence has been reconstructed based on eight full-length copies; they are ~92% similar to the consensus sequence. One copy has been inserted into Alu-Y repeat. Harlequin was built up from several different retroviruses including HERVE, HERVI, HERV17 and MER4I-group sequences. We suggest that shuffling of non- homologous endogenous retroviral sequences may generate mosaic retrovirus-like elements. Presumably, the shuffling occurs in virions where RNA genomes of different retroviruses could be packed in together. Self-catalytic RNA recombinations or jumping of reverse transcriptase between non-homologous RNA molecules may induce the shuffling. |
| Sequence |
TTTCTTGGTTCCCTGACCGGGAAGCGAGGTGATTAACGGACGGTCGAGGCAGCCCCTTAGGCGGCTTAGGCCTGCCCTGTGGAGCATCCCTGCGGGGGACTCCGGCCAGCCTGAGCGACGCGGATCCTGAGAGCGCTCCCGGGTAGGCAATTGCCCCGGTGGAACGCCTCGCCAGAGCAGCGCGTGGCAGGCCCCCGCGGAGGATCAACGCAGTGGCTGAACACCGGGAAGGAACTGGCACTTGGAGTCCGGACATCTGAAACTTGGTAAGACTGGTCTTTGGAACTTGCCCCACTCCATTTGAGTGGAAGCGTGGCCTGATCACCCACGGCGTGCCTGTACCGGCACTTTGGTTTTTGTTTTTGACTTGACTTGGATTGCTTGATACTTTGGTTTTGGTTTTGACCTGGCTTGGATTTCTGGATACTCTGATTTTGGTTTTGATTTTGGTTTGGTGTAAACTGCAAAAGTGTGTGTGTGCCCTTTTTACCCGTTCTTTGTTTTGTGGTGTGCGTGTGGTGTGAGCGTGGTGTTTTGTCTCGAAGAAGCATGGGTCAGGCACAAAGTAAGCCCACCCCACTAGGAACTATGTTGAAAAATTTCAAGAAAGGATTTAAGGGAGACTACGGNGTTACTATGACACCAGGAAAACTTAGAACTTTGTGTGAAATAGACTGGCCAGCATTAGAGGTGGGTTGGCCATCAGAAGGAAGCCTGGACAGGTCCCTTGTTTCAAAGGTATGGCACAAGGTAACCTGTAAGCCAGGGCACCCAGACCAGTTCCCGTACATAGACACTTGGTTACAGCTGGTTTTAGACCCCCCGCCCCCACAGTGGTTGAGAGAACAGCAGCATAAGCGGCTGGCAGAGGCAAGGAAAGACCAGCAGAGAGANNGAGAGAGGAAAGAGACAGAGAGGAAAAGAGGCAAAGAGAGAGAGGAAGAGACAGAGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAAGGAGAGAGAAAGAGAGAGGCAGAGAGAGAGGAAGAGACAGAGGCAAAAGGAAAGTCAAAGAGAGANAGAAAGTCAAAGAGAGAAAGAAAGAGAGAGATATACAAGTAGTTAAGAAAAAAAACAGTGTACCCTATTCCTTTAAAAGCCAAGGTAAATTTAAAACCTATAATTGATAATTGAAGGTATTCTCCGTAACCCTATAACACTCCAATACCACTTTGTTGTCAGTGTAAACAAGGGCGTATCCCGAAAGCACTGAGGCCTTCCTATCAAAAATCCTTAACCCAGTAACCCGCGGATGGCCCAAATGCATTCAATCTGTAGCGGCAACTGCTTTGCTAACAGAAAAAAGTAAAAAAAATAACTTTTAGAGGAAACCTCATTGTGAGCACACCTCACCAGTTCAGAAGTATCCTAAGGAAAAAAAAAAAAAAAAGGATGATTTAACATTAACCACTGAAAATTCCCTTAACCCAGCAGGTTTCCTAACAGGGGATCTAAATCTTAATTACCATACAAAGGTCCGACCAGACCTAGGAGGAACTCCCTTCAGGACAGGACGATAGATGGTTCCTCCCGGGTAATTGAAGAAAGAAAAAAAGCCATCTATACCAATTCTAAGTTAATTTGGACTAAACAAGGTCTTATTAATAGCAAAGGATAATTGAAATCCCAAACTTACAAGGTTTTCAACAAAAGTAAAGTTTGCTAAAAGTTAACAGTGTAACATGTATTATAGTAACTTCTAATCTTGTGGCCTTAGACAGTCTAGTCCACAGACATAAAGGAAGTTCGCTTTGGAAAAGAATGGTTATCATCTTCGAAAAAAAAAGAGAGGAAAGGGGGGGCAGAATTTATGTAAAAAGAGTGTTATATGGTAAATTCTTGTCCTGAAATAAATTAACTGGTTGTTTAAAGAAAGAAATGTTTGTAATAAGTCAGAAAGTTGAGGCATGTCGAAGAATTGTCTGCGAAAGTCGTGAAAGAAAAAAATGTTATAAAAAAAGAATTTATGCAAGAAATGTTGTATAATTTAAAAGTAATTAGGCCTCCTGAATGTAAAACTATTGAAAAAACAGTTTATGTGCAAGGTGTATAAGGAAAGTAAAATATACCTTTGGTAAAAGGATTATAAGGAGGCATAAGAATGTGGATTTTTACCTACATTAAAAGGTTAAAAAAATTATTGTTTTGAAGGTTTAAGCAAGTTTTAAAACGTTAATTGTAAAGAAAATTCTGTGTGTAAACATATTAGCTAAAGTTAAAGAGGTATCATCCAGTTTTTCTGTGAACTGGACATTAAAGTAAAAACGCAACGGGTTTTTCTTAAAGCACCAACCTGCTCTTTAACAAAAATTATAAAAGGTTAAAAAGAGTCTATAAAAATCTTACCTTATGGTCAAACATTAAAAATTGGATAAATATGTCTACAAGGTTTTATTAAAATTAAGTTTAACATTAATAACACACTAATATAAAGGTGAAATTTAGCTTATCTGGTATAAAAATCATACAAGAAGCATTGTTAAATATAAAATGGTGTTTGGCTTTCTTTGGTCTAAAAACTAATAAAAATAGGTGCTAAAGGAAATTTCTCAGTAAAAAGGCACCAAGGACTATAAAGTCCACTGCCGATGTCCCCACATTTAAAACAAAAGGTCAATTTCTTAGAAATTATATACTTGGTTTATCTTCCACTTTCCTTTCCCTCAAAACTAAAAGTCTTTTAGCACATGTACCACCCCTAGAATTTCCGGTAAACCAGCACCAGCCTGAAGATCACGTTCTCATCAAAGGGTGGAAAGAAGGAAAACTCGAGCCAGCCTGGGAAGGACCCTACCTTGTGCTGCTAACCACCGAGACTGCTGTTCGTACAGCGAAAAAGGGATGGACTCATCACACCCGAGTCAAGAAAGCGCCACCCCCTCCAGAGTCGTGGGCCATAGTCCCAGGGGAAAACCCTACCAAACTAAAGCTAAGAAAAATTTAACTCTTTCATCTATTCTATTACTCTTTCTTCTTTCCTCGCTCTATTGCTGACCATCTAGTTATTAACATAACCAAGTCAATTTCGCCTCAAACTATTGCATTTAATGCTTGCCTTGTTATACCCTGTGGGGACTTGCCAAGTCAAAGACAGCTCTCTACTTCAGAAAAGTACCTCTGTCCCTCCTGACTCTCCTCAGACTGGGCATTAGTAAATTAGGACCATTTAATCCGGGGAGATTTCGATAAAGACCCCAGTGTCAACCAGGAGTCTTGCCCCCCGATGTAGAGCTTTTATGCCGTAGTTGGTCCAACGTTCTGTGGACCACTAAAGAGCAAGGATGGACTGCCCCAACCGGTTTTTGTAATTTCCTAAAACCATACATTCATTTTACTAGAGGATCATAGAAGTTAAAGACTTAAAACAAACTTTGGCAATTAAGACAGGATACCAAGATGCAAATGCCTGGTTGGAATGGATCAAATATTCCATCCGCACGTTAAACAAAAGCAATTGTTATGCTTGTGCACATGGCAGGCCAGAGGCCCAGATTGTCCCCTTTCCACTAAGGTGGTCCTCCAGTCGACCAGGCGTGGGCTGCATGGTAGCTCTTTTCCAGGATTCTACAGCCTGGAGTAATAAGTCGTGCCAAGCTCTCTCTGCTATATCCCGAAGTCCGGCACCCTGCGGGTCAGCCCCCGAGGGCCATCCAGCTTCCGTCTCCCAACACTAAGTTCACTTCGTGTCTCTCACGACAGGGAGGAAACTTAGCGTTCCTTGGAGACCTGAAGGGATGCAGTGAGCTTAAGAATTTTCAAGAGCTTATCAATCAGTCAGCCCTTGTTCATCCCCGAGCGGATGTGTGGTGGTATTGTGGTGGACCTTTACTGGGCACTCTGCCGAATAACTGGAGTGGCACTTGTGCTTTAGTCCAATTGGCTATCCCTTTCACCCTGGCATTTCATCAACCAGAGGGAGGAAAAATAAGACATCGTAAAGCGAGAGAAGCCCCTTATGGGTCTTTCGACTCTCACGTCTATTTAGACGCAATTGGAGTCCCACGGGGAATACCAGATCAATTTAAAGCTTGAAATCAAATAGCTGCAGGATTTGAGTCAATATTTTGGTGGGTGACAGTTAATAAAAATGTAGATTGGATAAACTACATCTATTACAACCAACAGCAACGAGCTTTTCATGAGTTAAAAGAAAAACTCATGTCGGCCCCAGCCCTGGGGCTACCTGACCTGACAAAACCCTTTACACTCTATGTGTCAGAAAGAGAAAAAATGGCAGTTGGAGTTTTAACCCAGACTGTGGGGCCCTGGCCAAGGCCAGTGGCCTATCTCTCAAAACAACTAGACGGGGTTTCCAAAGGCTGGCCCCCATGTCTAAGGGCCCTGGCAGCAACGGCCCTGTTAGCACAAGAAGCAGATAAACTAACCCTTGGGCAAAACCTGAATATAAAGGCCCCCCATGCTGTGGTAACTTTAATGAATACCAAAGGACATCATTGGCTAACGAATGCTAGATTAACCAAGTACCAAAGCTTGCTATGTGAAAATCCCCGCATAACCATTGAAGTTTGCAACACCCTAAACCCCGCCACCTTGCTCCCGGTATCAGAGAGCCCAGTTGAACATAACTGTGTAGAGGTGTTGGACTCAGTTTATTCTAGCGGGCCCAACCTCCGAGACCATCCTTGAACATCAGTAGACTGTGAGCTGTACGTGGACGGGAGCAGCTTCGCCAACCCCTGCAAAGTGACTCTGAAGAAGACGACAAGCCCTGCTCCAGTCACACCCGGAAGCTGACTGGTCCACGCACGGCCGAAGCATGAGAAAACTCATCGCGGGACTCATTTTCCTTAAAATTTGGACTTGTACAGTAAGGACTTCAACTGACCTTCCTCAGACTGAGGACTGTTCCCAGTGTATACATCAAGTCACTGAGGTAGGACAAAAGGTTGCTACGGTCCTATTATTTTATGGTTATTATAAGTGTACCGGAACTCTAAAAAGAACTTGTTTGTATAATGTTATTCTATACAAGGTATGTAGCCCAGGAAATGACCAACCTGATGTGTGTTATGACCCATCTGAGCCTCCCATGACCACAGTTTTTAAAATAAGATTAAGGACTGAGGACTGGTGGGGGCTCATAAACGATACGAGTAAAGTGTTAGCCAAAACAGAAGAAAAAGGGGTGCCCAAACAAGTCACCTTGAAATTTGATGCCTGTGCTGTCATTAATAGTAATAAGTNTAGGAATAGGATGTGGTTCTCTTAATTNNAGGAAAGAGGCTATATGGCAGAAAATAAGTACATTTGTCATGAATTAGGACTGTGTGGAAATAAATGTGGATACTGGTCTTGTGTCATTTAGGCTACTTGGATAAAAAATGAAAAGGATCCTGTCCACCTTCAGAAAGGGAAAAGTGGCCCTTCCTGTACCAGTGGTCAGTGTAACCCCTTAGAACTAGTAATAACCAACCCCCTTGATCCTCGCTGGAAAAAAGGGGAGCGTGTAACCCTAGGAATCGATGGGGCCGGACTGGATCCTCGAGTAAATATCGTGGTTCGAGGAGAAGTTTATAAACGCTCTCCTGAGCCAGTATTTCAAACCTTCTATGATGAACTGAATGTGCCAGTACCAGAAATTCCAGGAAAAACAAGAAATTTGTTTTTGCAATTAGCCGAGCATGTAGCCCAGTCTCTCAATGTCACTTCATGTTATGTATGTGGAGGAACTGTAATGGGAGATCAATGGCCATGGGAAGCCCGAGAATTAGTACCTACAGACCCAGTTCCTGATGAATTCCCGGCTCAAAAGAATCACCCTGATAACTTCTGGGTCCTAAAAGCCTCAATCATTAGACAATACTGTATAGCAAGAGTGGGGAAGGACTTCACCCTTCCCGTGGGAAGACTCAGCTGCCTTGGGCAAAAACTGTATAATAGTACTACAAAAACAGCCACCTGGTGGAGTTCAAACCACACTAAGAAAAATCCATTTAGTAAATTCCCAAAGTTGCAAACCGTGTGGACCCACCCGGAGTCCCACCGGGACTGGACAGCCCCCACTGGATTATACTGGATATGTGGGCATAGAGCTTACGCCAAATTACCCGACCAGTGGGCAGGTAGTTGTGTTATTGGCACTATTAAACCATCTTTCTTCCTACTGCCCATAAAGACAGGCGAACTCCTGGGCTTCCCTGTCTATGCTTCCCGCGAAAAGAGAAGCATAGCTATAGGAAATTGGAAAGATGATAAATGGCCCCCTGAGAGAATCATACAATATTATGGGCCTGCTACTTGGGCACAAGACGGCTCGTGGGGATACCGGACCCCCATTTACATGCTCAACCGAATCATACGGTTACAAGCTGTCTTAGAAATAATCACTAATAAGACCGGCAGAGCCTTGACTATTCTGGCCCGGCAAGAAACTCAGATGAGAAATGCTATCTATCAAAATAGATTGGCTCTCGACTACTTGCTAGCAGCTGAAGGAGGGGTCTGTAGGAAATTTAACCTTACTAATTGCTGCCTACACATAGATGATCAAGGGCAAGTAGTTGAAGACATAGTTAGAGATATGACAAAACTGGCACATGTGCCCGTGCAAGTGTGGCATGGATTTGATCCTGGGGCCATGTTTGGAAAATGGTTCCCAGCGCTAGGAGGATTTAAAACTCTTATAATAGGAGTTATAATAGTAATAGGAACCTGCTTACTGCTCCCTTGTTTGCTACCTGTACTTCTTCAAATGATAAAAAGCTTCATCGCTACCTTAGTTCACCAAAATGCTTCAGCACAAGTGTACTATATGAATCACTATCGATCTGTCTTGCAAGAAGACATGGGTAGTGAGAATGAAAGTGAGAACTCCCACTANTGAGTGAGATTCTCAAAGGGGGGGAA
|
TF motifs of the concenus sequence
Use FIMO to detect transcription factor motifs in the concenus sequence of the TE family.
| TE_family | TFBS | Start | End | Strand | Score | Matched sequence |
|---|---|---|---|---|---|---|
| Harlequin | BPC5 | 984 | 1013 | + | 35.76 | GGAGAGAGAAAGAGAGAGGCAGAGAGAGAG |
| Harlequin | BPC1 | 987 | 1010 | + | 31.38 | GAGAGAAAGAGAGAGGCAGAGAGA |
| Harlequin | BPC1 | 1059 | 1082 | + | 30.29 | AAGAGAGAAAGAAAGAGAGAGATA |
| Harlequin | BPC6 | 1061 | 1081 | - | 27.59 | ATCTCTCTCTTTCTTTCTCTC |
| Harlequin | BPC1 | 997 | 1020 | + | 26.85 | GAGAGGCAGAGAGAGAGGAAGAGA |
| Harlequin | BPC1 | 985 | 1008 | + | 26.24 | GAGAGAGAAAGAGAGAGGCAGAGA |
| Harlequin | BPC1 | 1061 | 1084 | + | 25.50 | GAGAGAAAGAAAGAGAGAGATATA |
| Harlequin | BPC1 | 941 | 964 | + | 25.44 | AAGAGACAGAGAGGAAGAGACAGA |
| Harlequin | BPC1 | 1057 | 1080 | + | 24.88 | CAAAGAGAGAAAGAAAGAGAGAGA |
| Harlequin | BPC1 | 983 | 1006 | + | 24.56 | AGGAGAGAGAAAGAGAGAGGCAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
