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 | DIV1 | 300 | 310 | + | 14.76 | TGGATAAGATA |
| MER11D | ZNF135 | 822 | 835 | + | 14.68 | TCTCGACCTGCCGA |
| MER11D | Sox11 | 845 | 852 | + | 14.51 | GAACAAAG |
| MER11D | TBF1 | 355 | 362 | - | 14.43 | AACCCTAA |
| MER11D | KLF5 | 699 | 708 | + | 14.39 | CCCCCGCCCT |
| MER11D | TCFL5 | 130 | 137 | - | 14.38 | TCACGCGC |
| MER11D | ANL2 | 721 | 730 | - | 14.36 | GCATTTATTA |
| MER11D | AT1G74840 | 298 | 306 | + | 14.36 | TATGGATAA |
| MER11D | DREB2A | 768 | 776 | + | 14.32 | AAGGCGGTG |
| MER11D | GLYMA-08G357600 | 73 | 81 | + | 14.30 | TTGCATGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
