CR1_Amni-1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0004193 |
|---|---|
| TE superfamily | CR1 |
| TE order | 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 | BPC1 | 867 | 890 | - | 1.94 | GACAGGGTAAAAAGGAGGGACTGA |
| CR1_Amni-1 | BPC1 | 869 | 892 | - | 0.03 | GGGACAGGGTAAAAAGGAGGGACT |
| CR1_Amni-1 | BPC1 | 799 | 822 | + | -0.02 | GAAAGGAGAAGAGTTAGAGGGGAC |
| CR1_Amni-1 | ZNF143 | 739 | 754 | - | -0.24 | GTCCCGCCATACCTCT |
| CR1_Amni-1 | Rarb | 710 | 726 | + | -0.45 | AGGTCCAGAGAAGGGCA |
| CR1_Amni-1 | TCP14 | 748 | 765 | - | -1.37 | ATCATACGTAAGTCCCGC |
| CR1_Amni-1 | Rarb | 1008 | 1023 | + | -4.00 | GGAGGTCATCGAGTCA |
| CR1_Amni-1 | RARA | 900 | 917 | + | -11.38 | GAGAACAAGGGGTCACTC |
| CR1_Amni-1 | DAL81 | 1248 | 1266 | + | -52.00 | CACTGCCGGAGGCAGGATA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
