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 | ZKSCAN1 | 428 | 436 | + | 14.05 | ACAGTAGGC |
| L2b_3end | Klf6-7-like | 151 | 170 | + | 14.03 | GCCTGGAACGCCCTTCCCCA |
| L2b_3end | usp | 243 | 251 | - | 14.00 | GGGGTCAGG |
| L2b_3end | ZKSCAN5 | 220 | 228 | - | 14.00 | GGAGGTGAC |
| L2b_3end | ci | 279 | 289 | + | 13.93 | GGCCCCCCCAG |
| L2b_3end | nhr-6 | 216 | 223 | + | 13.81 | AAATGTCA |
| L2b_3end | TFAP2A | 118 | 128 | + | 13.80 | CGCCTCAGGGC |
| L2b_3end | l(3)neo38 | 281 | 287 | + | 13.75 | CCCCCCC |
| L2b_3end | ZBED4 | 10 | 19 | + | 13.62 | CTGGCCCCGC |
| L2b_3end | TFAP2C | 118 | 128 | - | 13.62 | 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.
