L2b_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000360 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Theria_mammals |
| Length | 466 |
| Kimura value | 32.92 |
| Tau index | 0.7773 |
| Description | 3' end of L2 (LINE2) retrotransposon, L2b_3end subfamily |
| Comment | L2 3' region. Starts at 2910 of L2 consensus with ~170 bp overlap. MIR and MIRb share 3' terminal end homology over ~50bp. |
| Sequence |
TCGCACGATCTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGAAT
|
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 |
|---|---|---|---|---|---|---|
| L2b_3end | PK19717.1 | 278 | 286 | + | 15.24 | GGGCCCCCC |
| L2b_3end | TFAP2A | 119 | 127 | + | 15.22 | GCCTCAGGG |
| L2b_3end | TFAP2C | 119 | 127 | - | 15.20 | CCCTGAGGC |
| L2b_3end | ZNF770 | 28 | 35 | + | 14.94 | CGGCCTCA |
| L2b_3end | PRDM9 | 16 | 35 | - | 14.66 | TGAGGCCGGAGAGGTAGCGG |
| L2b_3end | ASH1 | 257 | 266 | + | 14.64 | CCGGGTCAGG |
| L2b_3end | ZNF692 | 276 | 283 | - | 14.58 | GGGCCCAG |
| L2b_3end | ZNF320 | 267 | 286 | - | 14.57 | GGGGGGCCCAGAGGAGGGCG |
| L2b_3end | ZNF257 | 114 | 123 | - | 14.34 | GAGGCGGGAG |
| L2b_3end | TFAP2B | 118 | 128 | - | 14.15 | GCCCTGAGGCG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
