L4_A_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000364 |
|---|---|
| TE superfamily | RTE-X |
| TE class | LINE |
| Species | Eutheria |
| Length | 4990 |
| Kimura value | 35.46 |
| Tau index | 0.8282 |
| Description | RTE-X retrotransposon, L4_A_Mam subfamily |
| Comment | L4_A_Mam is one of three ~80% similar L4 subfamilies. ORF1 (3-1490) is not fully reconstructed, though ORF2 (~1491-4805) may be. These proteins similar to those of RTEX-1_ACar in lizards and L5 in ancient mammals. The substitution level found in the Laurasiatherian reconstruction is ~37%. |
| Sequence |
AGTGGTAAAAATGCAGACATCCTCACCCCAGACGGGAGNANTNNAGGAGCCCCTCTCCCNCAGCTGCCCCTGCAGCTGCCTCCCTGGCTCCCTCNAACGGATCTCCTAGCCCANTTAAGGATGGCTCTCCAAAAANCCTCACCCCGGGAGACTCGGGAGGCCCACGGGTTNATTCTCCCCAGGGCTATAATTCTCNCCGTGCAGATGGCACNTTTGATTTNCTGGAACGGTGTTNCTTCCTGACATCTCACACCATCCAGNCCTTATATGAGGAGCTGCGCGTTTTAAAATCCGTGGTCTCCAANATACATAACCATTGGATTTGGGGCAAACCGTGCCAANAGCATGCCACGAGNCAGGAGGGGATGGTGGACGGGAGGTCACACCCGGGGAAGGGCCCTCCATGCANNGCCCCTGGCCTGACCCTGGTGAGGAACCAGGTGGCGNTGAACCTCCCGATGGACNCTCATGGGAGGAGGCACGGTAGAGGNTCCGTAGCCAGGCTCCTGGNACCGCTTTTACACCAGCCTGCTTCTAATNCACTTATTTCCAGGTCGNCCCACCTCCCTTCCCGGCAGGGTCATAGGAGGANCCTCTTGGCGTGCGGCTCTCCCCAGCTCCCTTCCCTCATTATGANGGTCAAGGAGAANCTGGCTAGAGCGNGGNTTATCCCGAATAGGGTTTTTAAAACGGGGTCAGCTGCGCCCCTGCTGGGCGGTTCTCTTAATTTGTCAGGACCTNTACTGGGCAACCCAGGTCCGCCTAGAANACCAGAACCTAAGGAGAAGGGGAGGCCCGTTTCACCTCCAGACCATGGGCCTTGGTCCCCCCTGGGAAAGTTCTCGGGGCACAGGGAGGTGGCTGAGGCTGGGTTCTCTCGATCCTTTGTCCGTCTCCCTAAGGGAGAACAGGACGCTATTCTGGGGAGGTTAGAGTCCCTGAAGGATNANTTAATCAACCTTCAGGGCCTAGGCCATAATGANAATACCCCTGACTTCATGNAGTTTTCTCCCATCGGANCTCCTGTTGGGTCCCCTTGNAGGACNCCANCGAAGGGGAGCTCTCTCCCCNGAGNGGGCCCCGCCCCATTACTGCACAATCTGACTGATTGCACCTCCCACCCAGCCTCAGGAAGTGACATCTCCCCTAGCCCTTTCCTGACTGAGAGACTGGACCCTCAGGCCGCCCCCACTCATTGCCCGACTCCNCTCTCCCNAGTGATAGTCCTNGAGAATCCTCCTTGTTTGGCTGACTCACCAGTAAGCCCCACCCCAGTGCAGGTGACCTGGCCCAGAAAGCCTGCAGACTCCCCTATTTCCAGGAACTGGTTAGACATGCTCCACCTTGGNCCGGATGAGCTTGGCTTGCCAGATCCGGGGCGAGCCGCTCCGCCGGAAGCAGCGGCCTCGGCGGGTGCTAAGCCACACGGTAAGGCCAACGGCTGCATTCTTTTAGATCCGGTAGACTCCCTGGAGCGTGCCCCTCAATGACTAAGATTCCTCTCCTGGAACGTGGCCGNTTGGGGCCCTAAAGGTAAGGACCCCGATGTGTCGGCTTTTCTGATGGGTTTTAATATTATATGCCTGTAAGAGACCTGGATTTTAGAACATTCATCTCCCCATATTCANGGTTTTAGACCTTTTATCTCTCCGGCTGTCGGGGAAAAAAATTTTGGCAGAGGTAAGGGTGNATTGGCCACCCTTATCTCCGTCAACCTCAGGGGGACTGCTGTCGAGCTNCCTGGCTCATATGACAGGAATCTTTTCCTTCTGGTTCTGATTCGGTTCCCTGGCAAGCTGGATGTGATTTGTCTTAACACTTACATTCCCCCTGCCAAGGCGCACGCTGTCTGCTTGGACATATGGTCTCATTTTNATGATCTTTTAACTTTTATTTATTCTACGTACCCCATGGCGGAGTTAATCATCTCTGGGGACCTGAACGCCAGGATTGGCGGCGGGTCCGATGGGGCCCTACCTGGAGCCGCTGAGGAATGGGAGGATTGCTTCCCCGTGGGCCATTCTTTTAGAGACAGATGTATTAACCTAAATGGAAAATTTCTCACCAAACTTATTTATGAACAGAACCTGGTGGTGCTGAATGGTAGCACGTGGGATAAATCTGGGGGAAATTTTACCCGTATCTCTACTCTGGGGGCCAGCATCATAGATTATATCATAGTTAGCCCCTCTCTGCTTACTACCATCCTTAGAATGGATATTCTGGACCGGGTAGAAAGTGATCATTTCCCTCTCGTTTTAACCCTTGGCGTAGCTGCCCCGGAGCCCGTCTGCACTCATGATTGGACTGGNGAGATTAGGGGGCTGAGAAGAGTAAGATGGACCGAGGGGCTTTCAAACTCTATTGGTGACCTNTTGCTATCCGAGGACTTCTTAAAACTCTGCCTCAGGTGCCTCGAGGGAGAGGTTTCTCCTCTCATCTCTTATCAACGGATTGCTGATAACTTAAAACCGGTTTTATCCGCACTGTGTCCCGGCAAACGTGGGACTTACCCTCCTAGTGCCTGGTTTGACAAGGACTGTCAGGNAGCCAAAAAAATCTTGGCCAGGTTAGTGAGGCGACATGCGAAACGAAAATCGGAAGAGGCCACCCGGGATCTTATCAAATTTAAATCTTATTATAAACTTCTCATTGCCTCGAAAAAACTCAGGTATAATAAATCCNTGTGGGAGGACCTGAGTTTGGCCGTTAGATCCGGTAATGAGGGCAGATTCTGGGACATAGTTACCCGAGGTATGAATTTGGTGAGTGAGGTCGTGGAAGCTCAGATCCCGGTTGACACCTGGGAGGCTTACTTTTCCCAGCTTTACAAACCAAGGTCAACTGCCCCGAACTTTGTAGATCCCAGGCCGCTTTCTGACTGGGTCCCGGTAATACTCCCTCATATNGTACAGTTGATTAAAAAGCTCAAGCTAAATAAAGCACCCGGGGAAGATTTCCTGCCTCCAGAACTGTTCAAGGACCGCTCTGAATGGTGGGCTCCGATCCTTGCCAATTTGTTTACCTTTATCAACTCTACGGGTATGGTCCCGTCTGGTTGGACCCAGAGTGTAGTCTATCCCATTTTTTAAAAGGGCAATCCTTTACTTCCCCCAAATTATAGACCTATTAGCTTACTAGACATTCCATCTAAAATGTATGCCAGTTTCCTTCTTGATAAATTGCAAGTCTGGGTTTCTCAGGCCAATATTCTACACGAGGAGCAGGCGGGCTTTAGGCACGGCTATTCCACTATTGACCACTGTTATACTCTTTATCACCTTGTGGAGAAATCTGTCAGGAACAACATAAGATTGTTTGCGGCTTTTATTGACCTTTCCTCGGCCTTTGACTCTGTGGACAGGAATCGGTTATGGGCTAAGCTGCATGAGCTCAATATAGACCCCCGGCTATTGATGCTCATACAGAACCTGCACCTTAATACCACCGCGAGAGTCAGGGTCAGTAGGAACGGTCTCTTGACGGATCAGATAACAATTTCCAGTGGGGTAAAACAGGGATGTGTTCTGCCTACCCTCCTTTTTAACTTGTATCTTAATGACTTGATACCACTTTTGGATGAGCTGGATGCATGCCCTCCTGCCATAGAGAACAGAAAGATAAGCATTCTCCTATATGCAGATGACATGGTTTTATTGTCACGAACTAGGAGTGGCCTTAATAGACAACTGGCCCTGCTATCTAATTACTGCCAGAAAGAANGGCTTNAGATCAACTATTCTAAAACCAAAGTCATCATTTTTGGTAGACGTCCTCCAACATTTAACTGGCTTATAGCTAATAACCCTATACAGCAAGTCAACTCATTCAGTTACCTAGGNGTACATTTTGCAACTAGTTTATCTTGGAGGGTTCACCAGGAAGTTACATTGCTCAAAGTTAGACGTTCTATGGGTGCTTTACTGAGATTTTTTTATGGCCGAGGTGGGCGTTTGGTNACACCTGCTTTAAAAATTTTCCAGGCTAAAATTATTGCGGCCATGCTCTATGGCGTAGAACTTTGGGGCCTCGATCGCCCATTTGTCCGTGTGTTGGAGCAGACCCAGAACTGTTTTCTGAGGAAAATCTTGGCCCTGCCCGCGGGTACTCCCTCGGCCCACCTCCGTGCGGAGGTGGGGTGGCCTTCTATTCAGGCACGCGTCCTNGTTAGGCTCCTCAATTTTCATAAGAGGATGTCAACCCTACCCCCAGCTCGGCTGACTGTTAAAGCATATGGNTCTGCNCTTAACCGGCAACATAGAATAGCTGCACTCCAGGTNCTTGTCAGAGAGTATAACCTCGAACTCNCTGCCGCCCAATACTTATCAAAAGCTCGGTTGAGAGAAATAATATTTATGGAGGATTGCCTGAAGGATATGCAGTCCATCCATTCCTCTAGATACTCTAAANTCTATCCTTGGATTAAGCCAGACCANCAGAGAGCTGCGTACCTGGACCGCATTGTTTTGGCTCCCTGCAGAATTGCTTTTACTGAATTGCGCTTTGGCGTTATGCCATCGGCCTACATTGAGGGACGTTATAAGAAACAGCCCTATGAAACTCGTTACTGTATTTACTGTAAGGATGTTGTTGAGGACGTTGTTCATTACATCACACAGTGTCCTCTTTATGAGGACCCACGGGAGAAATTTCTCTCNGGTCTCAGTACCAGGAANAGCTGTGCTTCTCCTGAGCAACTGGTTTGTTTTTATCTTATGGACACTGTGAATCGTGTAACTGATCATGTTTCCCTCTTTGCNTTGGCTGCTAGGAAGCTCAGAGCCAAATTTGTGGCCCACCTCTAGCAANTGTACAGGACCTTATGGCATGCATTTTGTGTACTAACCTCACTCCTGGCTTCATCTTATTTTTCTACCCTTATTTTCCTTTTTCCTGATTTTTTAAATTTATATTTTTTAATTTTATTGTATGTATTTTTGTAAGCCGCCTTAAATCCTTTTTGGAACAAGGCAGGATATAAATAAATAAA
|
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 |
|---|---|---|---|---|---|---|
| L4_A_Mam | SOL1 | 2620 | 2634 | + | 18.07 | TTATCAAATTTAAAT |
| L4_A_Mam | KLF12 | 1079 | 1087 | - | 18.01 | GGGGCGGGG |
| L4_A_Mam | NFIX | 4504 | 4517 | + | 18.00 | TTGGCGTTATGCCA |
| L4_A_Mam | CDF5 | 4883 | 4903 | + | 17.95 | TTTCCTTTTTCCTGATTTTTT |
| L4_A_Mam | NHLH2 | 692 | 707 | + | 17.94 | GGGGTCAGCTGCGCCC |
| L4_A_Mam | KLF10 | 1079 | 1087 | - | 17.88 | GGGGCGGGG |
| L4_A_Mam | SP1 | 1079 | 1087 | - | 17.80 | GGGGCGGGG |
| L4_A_Mam | FKH1 | 3017 | 3029 | - | 17.65 | AAAGGTAAACAAA |
| L4_A_Mam | GRHL1 | 2469 | 2478 | + | 17.62 | AAACCGGTTT |
| L4_A_Mam | GRHL1 | 2469 | 2478 | - | 17.62 | AAACCGGTTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
