MER11D
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000718 |
|---|---|
| TE superfamily | ERV2 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 897 |
| Kimura value | 3.28 |
| Tau index | 0.9929 |
| Description | MER11D Long Terminal Repeat for HERVK11 endogenous retrovirus |
| Comment | MER11D is a retroviral LTR that has been proliferated by the HERVK- related retrovirus HERVK11. Generates 6 bp TSDs. MER11D is a very young subfamily of MER11 LTRs, 98% similarity to the consensus sequence. MER11D consensus sequence is only 64% similar to MER11A,B,C consensus sequences, which are also young subfamilies (~90% similarity). Note that MER stands for MEdium Reiteration frequency interspersed repeat. As such, MERs as a group are a grab bag of DNA transposons and retrotransposons. |
| Sequence |
TGTAGGGAGACCCCCTGAAACTATTGCTACGGAATAAAAGATGAAATGCTCCTGATTATTGTAAATACAAAATTGCATGCAGGATTGTGTAAAGACAATGCCAGGTTGGACTGCCAGAACGAGCCAACAGCGCGTGATGTGCTTCCCCCTGCAGAGAGCCTATGAATGGACGTGCAGTCAGGGAGGTTTCACATCACCAAGATTCCTATCCCAGAAAAGCAGATGTTCATAGCTCTGGGAATGGAATGCGACCCTTGTGGAGAGCCTATAAACGGACGCATGGGGGGCGCCTGTCCATATGGATAAGATAGGGCTATAAACGCCCTCATCTTGCCACGGCTCTTCTAGGCCTCTTTAGGGTTAAGGCATACTCCCTTCTGAGAATTTCTGGTCTAACCGGTTGTCTAGCTTCACGTCCTGTTTCTATGGATTGTTTGTAACCAGCTTTTGCTGCAACTGTTACTGCTGATTAATATCTTGCTAATCATAGGTTATGGAAAGACTGTGTTTCTGTTTTAAGGCTCTGTTAGAAATTACTGATGCACACACTATATTGTAAATTCTTATCTCTGTATACTGTACTTCTGCATACAGATGTACTGTACTTCTACATACAAATGTTATGTTAAAGAATTACTTCATCCCCATGTGACCATCTCACCTCATAATCAAATGACCCTAAATCCCTCACTAACCTACCCCCGCCCTCACTAAACTTAATAATAAATGCTGGTATATCCAGTGCATTGTTGGCACCGCGGGACCAGAAGGCGGTGACCCCCCTGGACCCAGCTTTCACTATCTTGTGTGTGTCTATTATTTCTCGACCTGCCGATCCGCCTGGGAACAAAGAGAGAGCCCCGTTGCATTGCGGGCTGCTGGCCAGATCCCGCAATA
|
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 |
|---|---|---|---|---|---|---|
| MER11D | SP9 | 700 | 709 | + | 14.20 | CCCCGCCCTC |
| MER11D | PK02532.1 | 471 | 478 | + | 14.19 | TAATATCT |
| MER11D | ZIM3 | 506 | 516 | - | 14.16 | AAACAGAAACA |
| MER11D | Klf6-7-like | 695 | 714 | + | 14.15 | CCTACCCCCGCCCTCACTAA |
| MER11D | KLF10 | 700 | 708 | - | 14.15 | AGGGCGGGG |
| MER11D | HHO2 | 199 | 206 | + | 14.10 | AAGATTCC |
| MER11D | HDG1 | 721 | 730 | + | 14.09 | TAATAAATGC |
| MER11D | FOXO1::ELK3 | 413 | 425 | - | 14.08 | AGAAACAGGACGT |
| MER11D | YAB4 | 300 | 310 | - | 14.02 | TATCTTATCCA |
| MER11D | AT3G10580 | 297 | 310 | + | 13.89 | ATATGGATAAGATA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
