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 | SPIB | 3610 | 3622 | + | 16.82 | CCAGTTCCTCTTT |
| HERV30 | Thap11 | 3642 | 3655 | + | 16.77 | ACCACACGTCCCAG |
| HERV30 | HSFB4 | 1200 | 1209 | + | 16.77 | GAAGTTTCCA |
| HERV30 | LFY | 430 | 448 | - | 16.73 | GTCTAACCGGCGGACATTA |
| HERV30 | LFY | 430 | 448 | + | 16.73 | TAATGTCCGCCGGTTAGAC |
| HERV30 | EREB29 | 8257 | 8266 | + | 16.70 | ACCGCCGCCC |
| HERV30 | BZR1 | 4532 | 4541 | + | 16.62 | CGCACGTGTG |
| HERV30 | cad | 1027 | 1037 | - | 16.59 | GGCCATAAAAC |
| HERV30 | ELF1 | 2903 | 2911 | + | 16.58 | CAGGAAGTG |
| HERV30 | ESR2 | 6277 | 6291 | + | 16.56 | AGGTCAGCCAGACCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
