AmnHarb1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001731 |
|---|---|
| TE superfamily | Harbinger |
| TE class | DNA |
| Species | Amniota |
| Length | 1444 |
| Kimura value | 32.87 |
| Tau index | 0.0000 |
| Description | AmnHarb1 subfamily |
| Comment | 21 bp TIRs. |
| Sequence |
AGGGNTGCGTTTTCAAAGCTTTATGTGCCACATGCGCATATAAAAACCAGGAAATGNGAATGCGTATGCACTGCACACGGAATTAGACACACATGACATATGTAAGCATTTTTAAAACGGGTGCAAATATGTACGTGCATGTACGCATGACTATTTCTGCACCTTGCAAAAATGGGCGGAGAGTGGGTGGAGCTACGATTATAGTCGCGCATTTGTAATTTTCAAAGGAAAATTGTGTGGGCAGCTTCCATTATGCCCGGGCAAATTTAGACGAATGAAAGCGTCGACTAAGTAATTNTTGATATTATATATGTGTATAAATTAAAGCAGGAAAGCCTCTAGTCACTCATTTTAGCTGCTAAAATGCCTCTAGGGGTTTGGATTAGAAGGAGGAGGACCCTTANAAGGATCAGAAGGCAATATCCCACGGGGGCAAATTGATACGTAGGAATACAGTAGCTATTCCTTTTTGGACCTCGCAGAGGAACAAGTTTTAGATAAANATACGACAAACAGACCATTTTGGATCTCTGTAAGAAGATTTGAAAAGTCAAACACACAGGAGCCATGCTTTACCTGTAATGGTAAAAATTACATCATCCGTAACCTTTTNAGCAACAGGCTTATTTCAAACAACAGTAACTTACAGATGCTATTCTAAGGAGAACCAGTCACTATATTTGTTTTCCTTTTGATATACAGCTGCAATAGCAAGCCATGCATGAATTTTATTAAGNCNTGATAATNTTCTATCAGTTCTAGGAGCTATAGANTGAACCCATATAGATAACTGGCTCAGCCTCAAAATGATAAACATGTCAAGATATGAAAATCATTTCATTCCTTAAAAATGAAATGAAGATGTGATTTGAAATGTCATGCTTTGGATGTATGAGCAANATTCCTATAATCAATCATCCAAAATAAACTGTATTATTTAGGAGCTATTTGAAGGCAGACAAGCTGAAAACATGTGTTTAAACATGCCAAACATGTTTAGAGTATCTCCTAAACATCTATATTACTTTTTCATACATACGTGTTGATTNTTGTTTCATATTTAGGGTTATTTACCTTACAAAGTAACTCAATACAATGAGCACACACTGCAAAACACTATAGAAAGGGAGTGTTTACATATGCTAATGACTTCCATNTAAGGAGCGCGTGACTAAGAGCTGAGAGAATGCGCGACTAAAACTGCCCGCTAGAAATCTTTGAAGATTCCCAGAAAAACTAGACGCGCAGGAAATGCCTGGTTGCTAGCATAACTGGTCGCGCAAATTTGCGCGGNCAGATANACAGATTTTCANNACTCATTTCACGNCTGTTACATCCTTTGAAAATANGGCAGTTTTTTCGGNTGCGCGCAGTTGCGCATCCGANACACATGCTAGTCGGGCAAAATGACTTGCCCGCGATTTTTTGAATATCTAGCCCTATG
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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 |
|---|---|---|---|---|---|---|
| AmnHarb1 | WRKY71 | 546 | 555 | + | 15.83 | AAAAGTCAAA |
| AmnHarb1 | Foxl2 | 1131 | 1140 | - | 15.83 | TATGTAAACA |
| AmnHarb1 | JUN | 591 | 600 | - | 15.78 | ATGATGTAAT |
| AmnHarb1 | POU1F1 | 1137 | 1150 | - | 15.69 | GTCATTAGCATATG |
| AmnHarb1 | WRKY59 | 546 | 555 | + | 15.63 | AAAAGTCAAA |
| AmnHarb1 | AGL1 | 573 | 588 | - | 15.62 | TTACCATTACAGGTAA |
| AmnHarb1 | TRB2 | 1059 | 1069 | - | 15.59 | TAACCCTAAAT |
| AmnHarb1 | FAR1 | 1163 | 1171 | - | 15.58 | TCACGCGCT |
| AmnHarb1 | AT1G72740 | 1059 | 1069 | + | 15.53 | ATTTAGGGTTA |
| AmnHarb1 | Crg-1 | 1067 | 1077 | - | 15.46 | AAGGTAAATAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
