HERV30
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000170 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 8308 |
| Kimura value | 6.06 |
| Tau index | 0.0000 |
| Description | Internal region of class I HERV30 endogenous retrovirus |
| Comment | Associated long terminal repeats are LTR30 and LTR30N2. Several deletion products exist and are included in the seed alignment, except for ERV30N1 which has a separate entry. Coding regions are 350-1231 (MC132-like), 1370-2827 (gag), 2831-6403 (pol; 1 stopcodon at 4039 should be TGG), and 7521-8231 (env). Closely related to HERV9 and HERV17 (HERVW) |
| Sequence |
TTTTGGCGAGCCAGCCAGGAGACTCCAGGAAAGGCATCTAGATCGTCACGCGGTGAGTACGATCGGACCTCTTTCGCTTGCTATTCTGTCCTGTCCTTCCTTAGAATTCGGAGGCTAAACACCGGGCACCTGTCGGCCACTTAAAGGCGATTAGCGCGGCCGCCGGACTAAAGACACGGGTGTCAGGCTGTCTGGAAAAGGGCTCTCTAACAACCCCCGACCCTTCGGGGTTGGGAGCATTGGTTNGCCTGGAACCAGTTCTAACTCTTTCGCTTTCCGTGGTGGTCCCGAAGTACACCCGGGAGTGCTCAGCGGACGTCTTAGTCTCCCAGATATCCTGGTTGAGACCATGGCCCCGCCAGAGGCTCCCCCTGCATGGGTTACTGAGCGTGAGACAGCCACATCTTCTGACTCCTGCCTCCTGGGTCCTAATGTCCGCCGGTTAGACTTCTTTCCTCATCTCGCAAGCAAGGTTATTCCCGCTAGGCAGGATCAAGATTCCCTATTTAGAAGTCTTAAATTCTTGGGGTGGCGCCCAGAAGATCCCTGTTCATGGTGCCCTCCAGGGTTTAGGCAGGTGTCGCCATTTGATGGCTATTTTGAAGGGCCAGTTCCCCACCATAGTGTATGGTCCCCCACATCAGGACAATTTAAAGACAGGTCTGTAATTTTCATGTGGATAGTAGAAGCCTTAGGGCATTTCCTCCATTGCTCCCCAGATAGACTTTCCCCTTCCTTGGGGCCTCTCAAGTACAATCTGTGGTGCATAGGCACGGGTCTTAGAGCCGTTGAATTGTTGTTTCAACCATTCAATAATTGGTATTGGANGGAAGAAAATATAGTCAGTTGGGACACAGGATACTGGTACCGCCTTGAGAGGGGGGCTTACTCCTTTGATGGCAAGTGGGGACAGAAGGCTAAAGTACAGCAGCTGTTCTCTCGGCCCTGGCCTAGAGGACATCCACCACCCCCTTTAAGCTTACTAAGCCTCCTGTCGCTAATTCAGAGATTTCTCCTTGAAGGACAGTTTTATGGCCAGGCCCACGTAAATTGGGCCTTAGCATGCAAGCATCAGTGGTGCCCCCGACCCAGGCCTTGCCACCCTGGAACAGGTAGGACGCGTTGGCAGAAGGACCACAATAAATCCAACAGTCCTTGTGCCCCATTTAGTGGTCAATGGGCGCACGGCAGGGGCAAGGGAAGTTTCCATCCCGCCGGTAAGCATGGTTAAATCCGGTAGATGGAGAGCTCAGGAAAAGCGGCCATGAGCTTTGAGCACAATTGGACCTGACCCTTAGGGGACGCCCTAAGGGAAGACGAGTCCCAGGACTAACCAGGGGTGCGGGCATCCCTGTGTTTAAAATTCCAGATGGGCACCACACCTTCAAAACCGGACACTCCCTTAAGATGTATCCTGAATAACTGGGACAAATTCGACCCTGAAACCTTAAAAAAGAAGCGGCTGATTTTCTTCTGTACCACTGCCTGGCCACAGTATTCCTTACAAAATGGAGAAACTTGGCCCCCTGAGGGAAGTATTAATTATAACACCCTTCTACAACTAGATCTTTTCTGTAAACAGGAAGGTAAATGGAGTGAAGTCCCTTATGTACAGGCTTTCTTTGCCCTTCGTGACAATACTGCCCTGTGCCAAGCCTGCAAGCTTTGCCCAAATGACAGAGGCCCACAATTGCCTCCATACTCAGGGCCTCTTCCCTCAGCCCCACTCTCCTCCCCCACTGACTCTCCTCCATCCGGCCCCACCGAAGTGTTAAAGGCACACCGGAAAGAGAACGTAAACTCCGCGAGCCAGGCACCCAAACTATGTCCCTTACAAGCAGTAGGAGGAGAATTTGGGCCCACCCGCGTGCATGCCCCCTTCTCACTCTCAGATTTAAAACAAATAAAGGCAGATTTAGGGAAATTCTCGGATGATCCTGATAACTATATAGATGTCCTGCAAGGATTAGGGCAGTCCTTTGATCTAACATGGAGAGATATCATGTTACTTCTTGATCAGACCTTAAGTCCTACTGAAAAGGAAGCAGCTTTAGCAGCAGCCCGGCAATTTGGGGATCTGTGGTACCTTAGCCAGGTAAACGATCGAATGGCCCTGGAGGAGAGGGAAAAATTCCCCACAGGGCAACAGGCAGTCCCCACTGTAGACCCTCATTGGGATACTGACTCAGATCATGGAGATTGGAGCCGCAGGCATTTGCTAACTTGCATTTTAGAAGGGTTGAGGAAGACTAGGAAAAAGCCTATGAACTACTCAATGCTATCCACAATTACGCAGGGAAAAGAGGAAAACCCCTCCGCTTTTCTAGAAAGGCTAAGGGAGGCCCTAAGAAAGCACACCTCCCTAACTCCGGATTCCNTGGAAGGCCAACTTATTCTAAAGGATAAATTTATCACCCAATCAGCGGCCGACATTAGGAGAAAACTCCAAAAGTCTGCCTTAGGCCCAGAACAAAATTTGGAGGCATTATTAAACCTGGCAACCTCGGTGTTCTATAACAGGGACCAAGAGGAACAGGCCAAAAGGGAAAAGCGAGATAAGAGAAAGGCTGCAGCCTTAGTCATGGCCCTCAGACAGGCAGACCTTGGTGGCTCAGAGGGAACCAAAAGAGGAGCAGGCCAATTGCCTAGTAGGGCTTGTTATCAGTGCGGTTTGCAAGGACACTTTAAGAAAGATTGTCCAACCAGAAACAAACCGCCCCCTCGCCCATGTCCAATATGCCAAGGCAATCACTGGAAGGCGCACTGCCCCAGAGGACGAAGGCCCTCTGGGCCAGAAGCACCCAACCAGATGATTCAGCAACAGGACTGAGGGTGCCCGGGGCAAGCGCCAGCTCATGCCATCACCCTCACAGAGCCCCGGGTAAGTTTGACCATTGAGGGCCAGGAAGTGGACTTCCTCCTGGACACTGGCGCGGCCTTCTCAGTTTTAATCTCCTGCCCCGGACGACTGTCCTCAAAGTCCGTTACTATCCGAGGAATCTTAGGACAGCCTGTAACCAGGTATTTCTCTCGCCTCCTCAGCTGCAATTGGGAGACTTTGCTCTTTTCACATGCCTTTCTTGTTATGCCCGAAAGTCCCACACCCTTATTAGGGAGGGACATATTAGCCAAAGCTGGGGCTATTATCTACATGAATATGGGGAACAAATTACCCATTTGTTGTCCCCTACTTGAAGAAGGAATCAACTCTGAAGTCTGGGCCTTGGAAGGACAATTCGGAAGGGCAAAGAATGCCCATCCAGTTCAAATCAGGCTAAAAGACCCCACCACTTTTCCTTATCAAAGGCAATATCCCTTAAGGCCTGAAGCTCACAAAGGATTACAGGATATTGTTAGACATTTAAAAGCTCAAGGCTTAGTAAGAAAATGTAGCAGTCCTTGCAACACCCCAATCCTAGGAATACAAAAACCAAATGGTCAGTGGAGACTAGTGCAAGACCTCAGAATCATCAATGAGGCAGTAATTCCTTTATATCCTGCTGTACCCAACCCCTATACACTGCTCTCTCAGATACCAGAGGAAGCAGAATGGTTCACTGTTCTGGACCTCAAAGATGCCTTCTTCTGCATTCCCCTGCACTCTGACTCCCAGTTCCTCTTTGCCTTTGAGGATCCTACAGACCACACGTCCCAGCTTACGTGGACGGTCTTGCCCCAAGGGTTTAGAGATAGCCCTCATCTGTTTGGTCAGGCACTGGCCCAAGACCTAGGCCAATTCTCAAGTCCAGGCACTCTGGTCCTCCAATACGCGGATGACGTACTTCTGGCTATCAGTTTGGAAGCCTCACGTCAGCAGGCTACTCTAGATCTCTTAAACTTTCTAGCTAATCGAGGGTACAAAGTGTCTAGGACAAAGGCCCAGCTCTGTCTACAACAAGTTAAATATCTAGGCCTAGTCCTAGCCAAAGGAACTAGGGCCCTCAGCAAAGAGCGTATTCAGCCTATACTGGCCTATCCTCACCCTAAGACATTGAAACAGTTGCGGGGGTTCCTTGGAATCACTGGCTTTTGCCGACTGTGAATTCCTGGATACAGTGAAATGGCCAGGCCACTCTATACCCTGATAAAGGAGACTCAGAAGGCGAATACCCATCTAGTAGAATGGGAACCGGAGGTGGAAACAGCCTTCAAAACTTTAAAGCAGGCCCTGGTACAAGCTCCAGCCCTGAGCCTCCCCACAGGACAAAATTTATCTTTATATGTCACCGAGAGAGCAGGAATAGCTCTTGGAGTTCTTACTCAGACTCGTGGGACAGCCCCACAACCAGTGGCATACCTAAGTAAGGAAATTGATGTAGTAGCCAAAGGCTGGCCTCACTGTTTACGGGTGGTTGCAGCAGTAGCCATCTTAGTGTCAGAGGCTATTAAAATAATACAAGGAAAGGATCTCACTGTCTGGACTACTCATGATGTAAGCGGCATATTAAATGCTAAAGGAAGTTTGTGGCTCTCAGATAACNGCCTACTCAAATACCAGGCACTACTCCTTGAGGGACCAGTATTTCAAATACGCACGTGTGCGGCCCTCAACCCTGCCACTTTTCTCCCAGAGGATGAGGAACCAATTGAGCATGACTGCCAACAAATTATNGCCCAGACTTATGCCACCCGAGAAGATCTCTTAGAAGTCCCCTTAACTAACCCTGACCTTAACCTGTACTCTGATGGAAGTTCATTTGTAGAAAATNGGGTACGAAAGGCAGGCTATGCCATAGTTAGCGATGCAGCAGTACTTGAAAGTAAGCCTCTTCCCCCAGGGACCAGCGCTCAGTTAGCAGAACTCGTGGCGCTTACCCGAGCCTTAGAACTGGGAGAAGGGAAAAGAATAAATGTGTACACAGATAGCAAGTATGCTTATCTAGTCCTACANGCACATGCTGCAATATGGAAAGAAAGGGAGTTCCTAACCTCTGGAGGAACACCCATTAAGTACCACAGAGAAATCATGGAGTTATTGCACGCAGTGCAAAAACCTAAGGAGGTGGCAGTCTTACACTGCCGGGGCCATCAGAAAGGTGAAGGAGAAGAAGCAGAAGGAAACCGCCGAGCAGACGCTGAGGCCAAAATTGCTGCCAGGCAGGACTTTCCTTCAGAAATGCCCATGGAAGGACCCCTGGTATGGAGCAACCCCCTCCAGGAGGTTAAGCCCCAGTATTCCCCAACTGAAACAGAATGGGGACTTTCACGAGGACATAGTTTTCTCCCCTCGGGGTGGCTAACAACAGAGGAAGGAAAGGTGCTCATACCTGAAGCCAGCCAGTGGAAAATACTTAAAACCCTCCACCAAACTTTTCATACGGGTATTGAAAGTACCCATAAGATGGCCACATCCCTATTTACAGGGCCAAACCTCCTCAAAACCATCCGGCAAGTAGTCAAAGCCTGTGAAGTGTGCCAAAAGAATAACCCCTTGGCCCACCGTAAGGCCTCTCCAGGAGGACAAAGAACAGGACATTATCCTGGAGAGGACTGGCAGTTAGATTTTACCCATATGCCAAAGTCAAGAGGATTTCAATACTTATTGGTCTGTGTTGATACCTTTACAAATTGGGTGGAAGCCTTCCCTTGTAGAACAGAGAAGGCCCAAGAAGTGGTTAAAGTCTTAGTTCATGAAATAATTCCTAGATTTGGACTTCCCCAAAGCTTACAGAGCGACAATGGTCCAGCTTTTAAAGCTACAATAACTCAAGGAATTTCCAAGGCACTAGGAATACAATATCACCTTCACTGTGCCTGGAGGCCACAATCCTCAGGGAAAGTCGAAAAGGCAAATGAAACACTCAAGAGGCATTTGAGAAAGCTAGCGCAAGAAACTCATCTCCCATGGCCCACTCTCTTGCCCATGGCCTTATTAAGAATTCGAAANTCCCCTCACAGAATGGGGCTCAGTCCATATGAAATGCTGTATGGATGGCCTTTTCTCACAAATGACCTCCTGCTCAATCAGGAAACGGCCAATTTAGTCAAAGATATAACTTCTCTGGCAAAATATCAACAAAACCTTAAAACTTTACCCGAAAGGTGTGACAGGGAAAAAGGAATAGAGTTGTTTCAACCAGGAGATCTAGTATTGGTCAAGTCTCTCCCCTCTACCTCTCCATCTATGGATCCCTTATGGGAGGGACCATACTCGGTAATCCTCTCTACCCCCACTGCAGTTAAAGTGGCAGGAGTGGAATCCTGGATTCACCACACCCGAGTTAAACCTTGGACACCTCCTGAGGAACTTACAGGATCATCANCTCAGGAGTCACAAGGTCAGCCAGACCAGCCTCGATACACCTGTCAGCCACTAGAGGACCTGCATCTCCTATTTCGGAAGGAAACATCTCAGACCAGAAAAACTCCTGCAGTTAATCCTGAAGAGGAACTTCTCTCTACCTAAAGGAGGATAAGTAAAAAAACCTACATGATCTTTGACATCTCTCCTTGCTCTCTTTAATGGAATCCTTCTACTGTTTCGTTACATTATTAAGCAGTATACTAACTATACTCTTTGCAGTAGGATTATATACTGTAGCTCCAGCCGGGACAAAAATCTTAACCACATCAACCTTTCTTCTATCGTCCTTCCTTCTAACAGCAATTTACTCCTTTTTCCCTCCTCTTTCCTACGACCGTTCCACCTACAACACGTCATGACTCCTCTTAGGCTTCCTGCCATCCTCTTCATACTCATGTCCCTTTCTCCAACTACNACACACNCCCCATGTCAGTGTGCCTCCCCTGGAGGAGTCAACCGGCATTCTCTCAGAAACTCTTGGGGATTAGGTAGCCCCTTCCAAGCACCCGCATCTTTTGCCGCGTATACTTACATGAGAAAAGAATGTTATAAAACTGCTTCTCTCTGCTCTCACAATGGCCGTACATATCACCAAGGAAAAATGATCCGAGCTGACTGCCCTGAGAAATGGGGGGCCAACGCTTGTTGGACATATTATACCCATATAGGTATGTCTGACGGAGGAGGCGTCCAAGATGAGGCTAAAGAACGGCATATCCAACAAGTAATTAAAAACTTAGTCCAGCTCTCCAGTACTCCCAGTCCATACAAGAAATTAGACCTTTCCAGGCTACAAGAAACCCTTAACTCTCATTCTCGTCTCTGGAGCCTGTTTAACACCACCCTTACAGGAATACAAGAGGCCTCTCCTAGTAATCCAACCAACTGTTGGATGTGTCTCCCCTTGCGTTTTCAACCATATGTCCCAGTCCCTGTCCCCGGACAGTGGAACTTATCCACCCCAGTCCTAAACACCACCAAATTAATCGGTCCCATAGTCACCAATTTACCAGCCACACAGGCCTCAAATCTCACATGCATAAACTTCAGCATGACTCTCAATAAGAACACCTCCCGATGTCAGTCCTGGATATCAGTAACCTCAGGTTTCACCTGTCTAACTTCAGGCATCTTTTTCATCTGTGATAACACAGCCTATTGATGCCTAAACGGCACTCCAAAAGAATTATGCTTTCTCTCCTTTCTAGCACCTCCCATGTCCATATATACTGAACAAGAGTTACAAAGTCTCCTTATACCCCAATCCCGCCACACACGAGCCCTTATTGTCCCTTTTATTGTAGGAGCCGGAATACTGGGCGGGCTTGGGACTGGAATTGGAGGCATAACCTCCTCCACCCAATTCTATTATAAATTATCACGAGAATTAAATGATGACATGGAACGAGTTGCCAACTCCCTAGTGACCCTACAAAGCCAGCTTAATTCTCTAGCTGCGGTAGTCCTCCAAAACCGAAGAGCCCTAGACCTATTAACAGCTGAAAGAGGAGGAACCTGCCTCTTCTTAGGAGAAGAATGTTGCTATTTCGTTAACCAGTCAGGAATCATTACTGAAAAGGTCAAAGAAATAAGAGAACGGATAGAAAGTAGGAAAAAGGAGCTTGAACACTCAGGACCCTGGAATATGTTTAACCAATGGATACCTTGGCTCCTCCCCTTTCTAGGCCCTGTGACAGCCATCCTACTATTACTCGCCTTTGGGCCTTGCATTTTTAACCTCCTTGTCAAATTTGTTTCCTCCAGGATCGAGGCCATCAAGCTACAAATGGTCTTACAAATGGAACCTCAAATGAGCTCAACTCACGGCTTCTACCGAGGACCCCTGGATCGACCCGCTGGTCCCTCGACTAGCCTAGAAAGTTCCCCTCTGGAGGACACCACAACTGCAGGGCCCCTTCTTCGCCCCTAACCAGCAGGAAGTAGCCAGAACGACCGCCGCCCAGTTCCCAACAGCAGTTGGGGTGTCCTGTTTAGAGGGGGGAC
|
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 |
|---|---|---|---|---|---|---|
| HERV30 | EWSR1-FLI1 | 6670 | 6687 | - | -14.99 | GGATGGCAGGAAGCCTAA |
| HERV30 | AT4G12670 | 3659 | 3687 | - | -15.91 | CTAAACCCTTGGGGCAAGACCGTCCACGT |
| HERV30 | ZSCAN16 | 7445 | 7462 | + | -16.09 | CTGTGATAACACAGCCTA |
| HERV30 | AT4G12670 | 6017 | 6045 | + | -16.98 | CAAAACCTTAAAACTTTACCCGAAAGGTG |
| HERV30 | BCL6B | 4006 | 4022 | - | -17.57 | TGATTCCAAGGAACCCC |
| HERV30 | BPC5 | 6038 | 6067 | + | -36.94 | GAAAGGTGTGACAGGGAAAAAGGAATAGAG |
| HERV30 | BPC5 | 3601 | 3630 | - | -39.45 | TCAAAGGCAAAGAGGAACTGGGAGTCAGAG |
| HERV30 | BPC5 | 6040 | 6069 | + | -42.49 | AAGGTGTGACAGGGAAAAAGGAATAGAGTT |
| HERV30 | BPC5 | 6105 | 6134 | - | -49.07 | AGGGATCCATAGATGGAGAGGTAGAGGGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
