CR1_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000110 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Mammalia |
| Length | 2204 |
| Kimura value | 35.29 |
| Tau index | 0.9420 |
| Description | Mammalian CR1 (Chicken Repeat 1) LINE |
| Comment | Mammalian remnant of an ancient LINE element first identified as CR1 (Chicken Repeat 1). The vast majority of CR1_Mam corresponds to roughly 2/3rds of ORF2 from CR1. |
| Sequence |
TAGATTGGCAAAATACCTCATCGGGACGAAATATAGAAGAGANGCTTTTCGATAAGACAAATNACCGCTTCCTAGAATAGGTAGTTTTAGAACCCACAAGGAAAGGAAATANACTGGACTTGGTTCTGAGNAGTGAACAGGAACTGGCGCAGGAAGTATCTGTGGGTGAACCACTATGTGACCAATAACGATTAAATTCAACATTCTGGCGGGAAAGGAAAACCAAAAAAAATCCATCACATGTTACTCAATTTTAGAAAAGGGAACTATGACAAAATGTGGGCATTAGTTAGGAAAAATGAAAAGNANAGTTTAAAAAGTAAATAACCCACAGGAAGCCTGGAGACTATTTNAAAACACCTTATTGGAAGCCCAGGAAAAATGTGTGCCANGGATCAAAAANACCAGGCGCTTGGAAAAAAAAATACCCNGCATGGCTAACTGGCAAAGTCAAAGAGGCTATTGTAGGGGAAAAGGCATCTTTCAAAAAATGGAAAGANAANTCCAAGTGAGGAGAACAGGGAAGCCCGCAAAGTATGGCAGGTCAGGTACAAACTAGAAATTAGGCGGGCCAAAAAAGAATTTGAGGAGCACCTTGCAAGGGACTCCAAAGCCAATAATAAAAGGTTCTTTAAATACATCAAAGGNAGGAAGCCAGCTAGAGAATCAGTGGGACCATTTGATGATCACGGTGCAAAAGGTGNACTCAAGATGAAAAAGGAGATAGCAGAGAGACTNAATGAATTCTTTGCTTCGGTCTTTACTGAGGAAGACGTTAGGGAGATTCCCACTCCCAAATTGTCTTTTGAAGCAGACAGGTCAGAGGTACTAGATCAAATAGTGGTAAACGCACAGGATGTTCTAGACCTAATTGACAAACTAGATGTAGATAAATCACCGGACCAGATGGCATCCACCCAAGAGTTTTGAAGGAACTCAAGGGTGAAACTGTTGACAAAATGTGTAACCTGTATTACAAACGGCCACTGTGCCNAGAACNAGTGTGTTCAATGGGCTCCATCCATAAGAAGGGCTCCAGAGGCCATGGAACTAAAGCCAGTGAGTCTCACTTCCATACCNGGCAAGCTGGTGGNATATAAGCAAAGAGTAGNACTNANCGCGCANNCAAACATAACCTACTAGGAGAAAGGCAACATGGTTTCTGTAAGGGGAAATCATGCCTGACTAATCTATTAGAGTTCTTTGAGGGGGTAAATAACATGTGGACAAGGAGAAACCAGTGGATATAATTTATTTAGACTTTCAAAAAGCCTTTGACAAGGTTCCACACCAAAACTTTATTTTTAAAAATTGAGTCACCATGGGATTNGGGGGAATGTTTTGTCATGGATAGGGAACTGGCTTAGAGACAGGAAACAAAAGGTAGAGAATAAACGGGCACTTCTCTGGATGGAGAAGTGTAAACAGTGGGGTCCCCCAGGGATCAGTGCTGGGACTAGTCTTATTTAACATTTTTATAAATGATCTGGAAGAGGGAGTGCACAGTGAAATCTCCAAGTTTGCAGATGACACTAAGCTCTTCCGGGTAGTGAAATGCCAAGCCGATGGGGATAAACTGCAGGAAGATCTCACGAGGCTGTGTGAGTGGGCAGAAAAGTGGCAGATGAGCTTCAGTGTGGGCAAGTGTAAGGTAATGCATTTAGGGAAAAATAATCCAAACTATACTTATAAGATGATGGGCTCTGAGCTATCAGTTACGACCCAGGAAAGGGATCTAGGAGTCATTGTAGACTGTTCCCTGAAGACATCAGCCCAATGTGCTGTAGCCAAAAAGGCCAACAAAATGCTGGGCATCATCAGGAAGGGTATTGGAAACAAAACAGAAAACATTATCCTACCTTTGTACAAAACCATGGTGTATCCGCACCTGGAATACTGTGTGCAGTTCTGGTCGCCGCATCCCTCAAGAAAGACATAACAGAGCTGAGAAGGGTAATTAAAATGATCAAGGGGATGGAAGGCTTTNATAAGAGGCTGAGCTGNTTTGTTTAAAACTTTAGTCTGGAAAGACGAAGGCTGAGAGGGGATATGATCAAAGTCTATAAAATCATGAAGGGTATGGATAAGGTGAACACGGACTTGTTCACCAAATCCCAGAATACTAGAACTAGGGCANCCTTTGAAGCTTGAAAGAAATTTTAGGGACAAATAAAAGAAAAGGCGTANACTCATTCTACAGAGGG
|
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 |
|---|---|---|---|---|---|---|
| CR1_Mam | E2F8 | 207 | 215 | - | 15.69 | TTCCCGCCA |
| CR1_Mam | Stat2 | 1838 | 1847 | + | 15.65 | AAAACAGAAA |
| CR1_Mam | Hnf1A | 638 | 647 | - | 15.62 | CCTTTGATGT |
| CR1_Mam | AT5G56840 | 2078 | 2091 | - | 15.59 | CACCTTATCCATAC |
| CR1_Mam | WRKY17 | 447 | 456 | + | 15.46 | AAAGTCAAAG |
| CR1_Mam | E2F7 | 204 | 217 | - | 15.41 | CTTTCCCGCCAGAA |
| CR1_Mam | WRKY3 | 446 | 456 | + | 15.41 | CAAAGTCAAAG |
| CR1_Mam | WRKY33 | 447 | 456 | + | 15.36 | AAAGTCAAAG |
| CR1_Mam | E2F6 | 208 | 215 | + | 15.29 | GGCGGGAA |
| CR1_Mam | TOD6 | 15 | 24 | + | 15.21 | ACCTCATCGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
