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 | FHY3 | 1163 | 1170 | - | 15.37 | CACGCGCT |
| AmnHarb1 | AG | 573 | 588 | - | 15.32 | TTACCATTACAGGTAA |
| AmnHarb1 | STAT3 | 1225 | 1233 | - | 15.20 | TTCTGGGAA |
| AmnHarb1 | STAT1 | 1225 | 1233 | - | 15.13 | TTCTGGGAA |
| AmnHarb1 | Stat5a::Stat5b | 1225 | 1233 | + | 15.12 | TTCCCAGAA |
| AmnHarb1 | POU3F4 | 1139 | 1147 | + | 15.10 | TATGCTAAT |
| AmnHarb1 | ATF4 | 591 | 600 | - | 15.09 | ATGATGTAAT |
| AmnHarb1 | ETV5::HOXA2 | 1144 | 1155 | - | 15.09 | TGGAAGTCATTA |
| AmnHarb1 | PAX6 | 713 | 726 | - | 15.06 | TTCATGCATGGCTT |
| AmnHarb1 | nub | 1139 | 1149 | + | 14.92 | TATGCTAATGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
