DNA1_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000113 |
|---|---|
| TE superfamily | Tc1 |
| TE order | DNA |
| Species | Eutheria |
| Length | 407 |
| Kimura value | 22.80 |
| Tau index | 0.0000 |
| Description | TcMar DNA transposon, DNA1_Mam subfamily (non-autonomous) |
| Comment | Present in ~200 copies in human and other placental mammals. It has imperfect TIRs and putative TSDs (TA, included in consensus). The sequence is a near perfect hairpin. |
| Sequence |
CAGGGTGTCCGAAAAGTCGGGAAACATAGGATAAACTTATTTTTAAACAGTATGTTAGTTACATTTTCAAATAATATGCTCAATATGTTTTTCTTCAACCTCCAGACACCTTTTCAGGTGAAGTACCTCTAAATTTAAAGCAATGGGTCCAATTGTTAATCTGAAAAAAGTACAATAAATACACTATTTTCCCTGTGTTTCCAGACTTTTTGGACACTCTGTAGTGTATTTATTGTACTTTTTTCAGATTAACAATTGGACCCATTGCTTTAAATTTAGAGGTACTTCACCTGAAAAGGTGTCTGGAGGTTGAAGAAAAACATATTGAGCATATTATTTGAAAATGTAACTAACATACTGTTTAAAAATAAGTTTATCCTATGTTTCCCGACTTTTCGGACACCCTG
|
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 |
|---|---|---|---|---|---|---|
| DNA1_Mam | GAF1 | 87 | 101 | - | 6.29 | AGGTTGAAGAAAAAC |
| DNA1_Mam | IRF2 | 339 | 354 | + | 5.75 | TGAAAATGTAACTAAC |
| DNA1_Mam | IRF2 | 54 | 69 | - | 5.75 | TGAAAATGTAACTAAC |
| DNA1_Mam | CG4360 | 172 | 184 | + | -0.62 | ACAATAAATACAC |
| DNA1_Mam | CG4360 | 224 | 236 | - | -0.62 | ACAATAAATACAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
