L1MD2_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000287 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 1106 |
| Kimura value | 22.37 |
| Tau index | 0.8586 |
| Description | 3' end of L1 retrotransposon, L1MD2_3end subfamily |
| Comment | ORF2 ends at bp ~675 |
| Sequence |
CTNGTATCTAGAATATATAAAGAACTCTCAAAACTCAACAGTAAAAAAACAAACAATCCAATTAGAAAATGGGCAAAAGACATGAACAGACATTTCACCGAAGAGGATATACAGATGGCAAATAAGCACATGAAAAGATGTTCAACATCATTAGCCATTAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACACACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGGCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTAAAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGTTTCTTATAAAACTAAACATGCANTTACCATACGACCCAGCAATTGCACTCTTGGGCATTTATCCCAGAGAAATGAAAACTTATGTTCACACAAAAACCTGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAAATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATACTACTCAGCAATAAAAAGGAACGAACTATTGATACACGCAACAACTTGGATGGATCTCAAGGGAATTATGCTGAGTGAAAAAAGCCAATCTCAAAAGGTTACATACTGTATGATTCCATTTATATAACATTCTTGAAATGACAAAATTATAGAGATGGAGAACAGATTAGTGGTTGCCAGGGGTTAGGGATGGGGGTGGNGNGGGGGAAGGGAGGTGGGTGTGGCTATAAAAGGGCAGCACGAGGGATCCTTGTGGTGATGGAACNGTTCTGTATCTTGACTGTGGTGGTGGNTACACGAATCTACACATGTGATAAAATTGCATAGAACTAAATACACACACACACACATGAGTACANGTAAAACTGGNGAAATCTGAATAAGATCGGTGGATTGTATCAATGTCAATTTCCTGGTTNTGATATTGTACTATAGTTNTGCAAGATGTTACCATTGGGGGAAACTGGGTGAAGGGTACACGGGATCTCTCTGTATTATTTCTTACAACTNCATGTGAATCTACAATTATCTCAAAATAAAAAGTTTAATTTAAAAAAA
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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 |
|---|---|---|---|---|---|---|
| L1MD2_3end | SP3 | 763 | 773 | - | 15.62 | GCCACACCCAC |
| L1MD2_3end | KLF16 | 763 | 773 | - | 15.59 | GCCACACCCAC |
| L1MD2_3end | DOF1.5 | 1081 | 1096 | + | 15.55 | AAAATAAAAAGTTTAA |
| L1MD2_3end | DOF5.1 | 1086 | 1104 | + | 15.33 | AAAAAGTTTAATTTAAAAA |
| L1MD2_3end | INSM1 | 723 | 734 | + | 15.29 | TGCCAGGGGTTA |
| L1MD2_3end | ZNF549 | 781 | 788 | - | 15.24 | TGCTGCCC |
| L1MD2_3end | CG3065 | 763 | 773 | - | 15.19 | GCCACACCCAC |
| L1MD2_3end | Bcl11B | 176 | 184 | + | 15.12 | AAACCACAA |
| L1MD2_3end | cg | 890 | 900 | + | 14.97 | ACACACACATG |
| L1MD2_3end | CDX4 | 556 | 564 | + | 14.91 | GCAATAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
