CR1_Amni-1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0004193 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Amniota |
| Length | 1319 |
| Kimura value | 33.73 |
| Tau index | 0.0000 |
| Description | CR1 LINE element |
| Comment | Possibly ancestral CR1 element to CR1 elements in Sauropsida and mammals. Closest matches to CR1-1(B)_CPB, which may be common to all turtles, CR1-15_AMi and CR1-14_Ami (common to all Crocodylia), the monotreme PlatCR1 and mammalian-wide CR1_Mam. Position 879-1172 was originally entered as X6B_LINE. The final 100 bp (pos 1223-1320) are very conserved amongst the descendant CR1 elements. For an orthologous copy in all amniotes see for example hg38 chr16:72,993,631-72,994,220. |
| Sequence |
GGTGGACATAATTTACTTGGATTTTCAAANAGCTTTTGATAAGGTCTCTCACAAAAGATTATTAAGGAAAATAAATAACCANAGGGTAAGGGGCAAAGTNCTGTCGTGGATTAAAAACTGGTTAAACGATAGGAAACAAAGANTCGCAGTGAATAGCCGTTCTCAGAGTGGAGAGAGGTTAATAGCGGGNTACCCCAGGGGTCTGTATTGGGACCGGTGTTATTTAATATATTTATTAATGATTTGGAGGAGGAAGTGGACAGTAAGTTGGCGAAGTTTGCTGATGACACTAAGTTGTTTTGGTTAGTAAAAACCACGGAGGATTGCGAGAAACTCCAGATGGATTTAAATACACTGGGGGATCGGGCAGCACGATGGCAGATGAAATTCAACTTGGATAAGTGTAAGGTAATGCACATTGGCAAAAATAGTCTAAACTTCTCATGTACGCCGATGGGCTCTGAACTTGCGGGATCCTCTGAGGAAAAAGACTTAGGAGTCATCGCGGATAGCTCAATGAAGACGTCTGCCCAGTGCGCAGCGGCAGTTAAAAAAGCAAATAGGATGCTTGGGTGCATTAAAAAGGGAATGGAAAATAATACAGAAAATATTATAATGACATTATATCGAACAATGGTACGCCCTCATCTGGAGTACTGTGTCCAGTTTTGGTCGCCTCACTTTAAGAAAGATATAGCGGAGATTGAAAAGGTCCAGAGAAGGGCAACGAAGATGGTTAGAGGTATGGCGGGACTTACGTATGATGAGAGACTGCAAAAACTAGGATTATTTAGCCTGGAAAGGAGAAGAGTTAGAGGGGACTTGATTGAGGTATTCAAAATTATGAAGGGTATAGTGAAAACTGATCAGTCCCTCCTTTTTACCCTGTCCCATAATACGAGAACAAGGGGTCACTCGATGAAATTAANGGNCGGTAAATTTAGAACAAATAAAAGGAAATACTTCTTCACGCAGCGTGTAGTCAGCCTGTGGAATTCACTGCCGCAGGAGGTCATCGAGTCAAATACTGTGGCTGGATTTTNAAAAGGGCTGGATAATTTTATGACCANTAATAACATTTGTAGTTATGCANGCTAAGATAAGGGTAATCAAATCTCATGCTTCAGGGCGTAAGCTGATCGCCTGCAGGGGTCAGGAAGGAATTTTTCCCCCACGTACAGCATTGCACAATTGGCTAGGTGCATTACGGGGTNTTTTCGCCTTCCTCTGAAGCATCAGGTATTGGCCACTGCCGGAGGCAGGATACCGGACTNGATGGACCAATGGTCTGATCCGGTATGGCAAATCCTATGTTCCTA
|
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_Amni-1 | Spi1 | 247 | 259 | + | 17.88 | GAGGAGGAAGTGG |
| CR1_Amni-1 | SPIB | 247 | 259 | - | 17.18 | CCACTTCCTCCTC |
| CR1_Amni-1 | ROX1 | 900 | 911 | - | 16.88 | CCCCTTGTTCTC |
| CR1_Amni-1 | CEBPA | 1183 | 1192 | + | 16.80 | ATTGCACAAT |
| CR1_Amni-1 | SOX14 | 628 | 636 | + | 16.11 | CGAACAATG |
| CR1_Amni-1 | DOF5.1 | 580 | 598 | + | 15.82 | AAAAAGGGAATGGAAAATA |
| CR1_Amni-1 | DOF5.8 | 580 | 598 | - | 15.77 | TATTTTCCATTCCCTTTTT |
| CR1_Amni-1 | CDX1 | 1059 | 1068 | - | 15.75 | GGTCATAAAA |
| CR1_Amni-1 | CTCF | 1142 | 1156 | + | 15.49 | GCCTGCAGGGGTCAG |
| CR1_Amni-1 | nhr-86 | 977 | 984 | + | 15.38 | GTGTAGTC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
