Eutr10
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001233 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Eutheria |
| Length | 790 |
| Kimura value | 34.25 |
| Tau index | 1.0000 |
| Description | Ancient interspersed repetitive sequence from eutherian mammals. |
| Comment | TGT...ACA termini, probable 5 bp TSDs, and ERVL-like ATTAAA poly A signal at the right place suggests this is an LTR. ERVL is a very uncertain assignment. Present at orthologous sites in elephant and humans, absent from opossum. |
| Sequence |
TGTNTTGGTAGGGGTCCCCGGGACAATCCCCTTTNTGGGGCCTGGGGCCCTCCAAGCAAATGCCACTTTGTAACGAGACTTTCTTTCTTTGGTCACCAGACTGTCCCCTAAATTAGTTGAAGCCTGTAGGCCTTAAATATAAAGCTGGCTGATGCAACTTGATTATAATGCAGCAGTTTGAATTTAGGCGCNAATGCTATGTTTGAAATGTAAGAGTGTGATTGGCTTTTAGCNATATATTTTAAAAGGATTGGTGGGTTACTTGTGCCTGGGCAGCCCAGCCCCTGAATGCCTGGCCACTCTCGATAAGAGTCAGGACTACACCCAGCTGGCCCCATAAAAGGGAGGGCCCGATGGCCGTCTCTCCGGGGCAGCCTGAGGCAACAGGACACGCACCCGGTCCGCGCTGCTGCTGTTGCACCTGCTGAGACCCGCTGACGGAAGTGCTGTCCCTCCCCTGACCGGACGAGGAAGGACCCAGTTTCCTCGGGGACCCGCAGGCTGCCGGAACAACTCCNCCCCCCCTTCTCCGCCATCAGCGTGCGCCGNACCCTGCCTGGAGTGGTGAGAAACTGTAACCCTTNACTCCCCTCTTTGGCTAGGGATCCTCCCCTTTCTTCCCCACTGGGTCTNGGGAGGACGGGAGGCGGCATTAAAGCTTGCTTNTGTTTTACCCATACCTTGTGAGTCTGTGTTCTCTGTGTAAAGGCCCACTCATTTAGAGGAAAAAGAACCTGCTCTTAGTTCCACCTCTGGAACTAGAAAATTAGTCTTTAATCAGACTAATACA
|
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 |
|---|---|---|---|---|---|---|
| Eutr10 | TFAP2C | 374 | 382 | + | 16.57 | GCCTGAGGC |
| Eutr10 | TFAP2A | 374 | 382 | - | 16.42 | GCCTCAGGC |
| Eutr10 | TFAP2B | 374 | 382 | - | 16.07 | GCCTCAGGC |
| Eutr10 | TfAP-2 | 374 | 382 | + | 15.56 | GCCTGAGGC |
| Eutr10 | TFAP2B | 374 | 382 | + | 15.56 | GCCTGAGGC |
| Eutr10 | TfAP-2 | 374 | 382 | - | 15.55 | GCCTCAGGC |
| Eutr10 | nhr-86 | 317 | 324 | - | 15.38 | GTGTAGTC |
| Eutr10 | SNAI3 | 417 | 425 | - | 15.36 | GCAGGTGCA |
| Eutr10 | Zic2 | 421 | 429 | - | 15.33 | CTCAGCAGG |
| Eutr10 | ERF5 | 524 | 538 | + | 15.29 | CCTTCTCCGCCATCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
