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
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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 | IRF8 | 506 | 518 | - | -3.98 | TAAAACAGAAACA |
| MER11D | ZSCAN16 | 518 | 535 | - | -8.81 | AATTTCTAACAGAGCCTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
