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 | TCX6 | 2620 | 2634 | - | 17.04 | ATTTAAATTTGATAA |
| L4_A_Mam | skn-1 | 3750 | 3763 | - | 17.03 | AAAATGATGACTTT |
| L4_A_Mam | NFIC | 4504 | 4518 | + | 17.02 | TTGGCGTTATGCCAT |
| L4_A_Mam | KLF5 | 1078 | 1087 | + | 17.00 | GCCCCGCCCC |
| L4_A_Mam | ZNF701 | 4632 | 4648 | + | 16.94 | GAGGACCCACGGGAGAA |
| L4_A_Mam | cad | 3932 | 3942 | - | 16.78 | GGCCATAAAAA |
| L4_A_Mam | AGL6 | 2041 | 2059 | + | 16.70 | TTAACCTAAATGGAAAATT |
| L4_A_Mam | ETV2::FIGLA | 431 | 443 | + | 16.67 | GAGGAACCAGGTG |
| L4_A_Mam | KLF5 | 1264 | 1273 | + | 16.67 | GCCCCACCCC |
| L4_A_Mam | ELF1 | 1129 | 1137 | + | 16.58 | CAGGAAGTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
