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 | DAL81 | 3217 | 3235 | + | -39.14 | ACGAGGAGCAGGCGGGCTT |
| L4_A_Mam | BPC5 | 4865 | 4894 | - | -44.16 | GGAAAAAGGAAAATAAGGGTAGAAAAATAA |
| L4_A_Mam | DAL81 | 4091 | 4109 | - | -51.72 | AGTACCCGCGGGCAGGGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
