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 | TFAP4::ETV1 | 1392 | 1404 | + | 17.60 | CCGGAAGCAGCGG |
| L4_A_Mam | SP2 | 1079 | 1087 | - | 17.56 | GGGGCGGGG |
| L4_A_Mam | DOF3.6 | 4883 | 4903 | + | 17.56 | TTTCCTTTTTCCTGATTTTTT |
| L4_A_Mam | SP4 | 1079 | 1087 | - | 17.54 | GGGGCGGGG |
| L4_A_Mam | TSO1 | 4901 | 4915 | - | 17.46 | AAATATAAATTTAAA |
| L4_A_Mam | KLF14 | 1079 | 1087 | - | 17.26 | GGGGCGGGG |
| L4_A_Mam | RAP2-12 | 1950 | 1960 | + | 17.20 | ATTGGCGGCGG |
| L4_A_Mam | ETV5::FIGLA | 430 | 443 | + | 17.12 | TGAGGAACCAGGTG |
| L4_A_Mam | NFIC::TLX1 | 4504 | 4517 | - | 17.08 | TGGCATAACGCCAA |
| L4_A_Mam | TCX2 | 2620 | 2634 | + | 17.06 | TTATCAAATTTAAAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
