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 | ARALYDRAFT_496250 | 282 | 289 | - | 16.55 | GGGACCAC |
| HERV30 | ARF10 | 7200 | 7210 | - | 16.50 | AAGGGGAGACA |
| HERV30 | Hnf1A | 1977 | 1986 | + | 16.49 | CCTTTGATCT |
| HERV30 | BAM8 | 4533 | 4541 | - | 16.46 | CACACGTGC |
| HERV30 | GCM1 | 6807 | 6816 | - | 16.45 | ATGCGGGTGC |
| HERV30 | CDX1 | 1028 | 1037 | - | 16.42 | GGCCATAAAA |
| HERV30 | ZNF257 | 3028 | 3037 | - | 16.37 | GAGGCGAGAG |
| HERV30 | TCP23 | 1856 | 1863 | + | 16.36 | GGGCCCAC |
| HERV30 | ASR1 | 1050 | 1058 | - | 16.33 | AGGCCCAAT |
| HERV30 | TGA4 | 3806 | 3816 | + | 16.27 | TCACGTCAGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
