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 | snpc-4 | 2422 | 2433 | - | 20.33 | ATGTCGGCCGCT |
| HERV30 | ETV5::FOXI1 | 1575 | 1586 | + | 19.83 | GTAAACAGGAAG |
| HERV30 | FOXO1::FLI1 | 1575 | 1587 | + | 19.07 | GTAAACAGGAAGG |
| HERV30 | Wt1 | 1731 | 1740 | + | 18.54 | CCTCCCCCAC |
| HERV30 | ERF::FOXO1 | 1575 | 1586 | + | 18.44 | GTAAACAGGAAG |
| HERV30 | BEH2 | 4532 | 4541 | - | 18.29 | CACACGTGCG |
| HERV30 | Spi1 | 3610 | 3622 | - | 18.19 | AAAGAGGAACTGG |
| HERV30 | FOXO1::ELK3 | 1575 | 1587 | + | 18.09 | GTAAACAGGAAGG |
| HERV30 | BEH4 | 4532 | 4541 | + | 17.98 | CGCACGTGTG |
| HERV30 | FOXO1::ELK1 | 1575 | 1587 | + | 17.98 | GTAAACAGGAAGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
