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
|
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 | GT-2 | 38 | 48 | - | 14.85 | TTTTTTACTGT |
| L1MD2_3end | cad | 555 | 565 | + | 14.81 | AGCAATAAAAA |
| L1MD2_3end | Klf6-7-like | 758 | 777 | - | 14.81 | TATAGCCACACCCACCTCCC |
| L1MD2_3end | knrl | 263 | 273 | + | 14.75 | AAACTGGATCA |
| L1MD2_3end | HOXD9 | 556 | 564 | + | 14.72 | GCAATAAAA |
| L1MD2_3end | Neurod2 | 111 | 118 | + | 14.69 | ACAGATGG |
| L1MD2_3end | luna | 765 | 773 | - | 14.67 | GCCACACCC |
| L1MD2_3end | FOXD3 | 42 | 55 | + | 14.67 | TAAAAAAACAAACA |
| L1MD2_3end | POU3F2 | 164 | 175 | + | 14.58 | AAATGCAAATTA |
| L1MD2_3end | NEUROD1 | 111 | 118 | + | 14.58 | ACAGATGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
