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 | SPL8 | 164 | 179 | - | 15.54 | TTTATTGTACTTTTTT |
| DNA1_Mam | SPL8 | 229 | 244 | + | 15.54 | TTTATTGTACTTTTTT |
| DNA1_Mam | SBP6 | 168 | 175 | + | 14.34 | AAGTACAA |
| DNA1_Mam | SBP6 | 233 | 240 | - | 14.34 | AAGTACAA |
| DNA1_Mam | fkh-3 | 160 | 167 | + | 13.74 | TCTGAAAA |
| DNA1_Mam | fkh-3 | 241 | 248 | - | 13.74 | TCTGAAAA |
| DNA1_Mam | ztf-6 | 159 | 167 | + | 13.47 | ATCTGAAAA |
| DNA1_Mam | ztf-6 | 241 | 249 | - | 13.47 | ATCTGAAAA |
| DNA1_Mam | DOF5.8 | 165 | 183 | - | 13.35 | TGTATTTATTGTACTTTTT |
| DNA1_Mam | DOF5.8 | 225 | 243 | + | 13.35 | TGTATTTATTGTACTTTTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
