LTR5_Hs
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000558 |
|---|---|
| TE superfamily | ERV2 |
| TE class | LTR |
| Species | Hominoidea |
| Length | 968 |
| Kimura value | 3.06 |
| Tau index | 0.9573 |
| Description | LTR5_Hs (Long Terminal Repeat) for ERVK endogenous retrovirus |
| Comment | A HERVK LTR (youngest subfamily < 1% div). |
| Sequence |
TGTGGGGAAAAGCAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATAGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGAGATTCTGTTAATCTATAACCTTACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCAACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCCTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCAGGGACACAAAAACTGCGGAAGGCCGCAGGGACCTCTGCCTAGGAAAGCCAGGTATTGTCCAAGGTTTCTCCCCATGTGATAGTCTGAAATATGGCCTCGTGGGAAGGGAAAGACCTGACCGTCCCCCAGCCCGACACCCGTAAAGGGTCTGTGCTGAGGAGGATTAGTAAAAGAGGAAGGAATGCCTCTTGCAGTTGAGACAAGAGGAAGGCATCTGTCTCCTGCCCGTCCCTGGGCAATGGAATGTCTCGGTATAAAACCCGATTGTATGTTCCATCTACTGAGATAGGGAAAAACCGCCTTAGGGCTGGAGGTGGGACATGCGGGCAGCAATACTGCTTTGTAAAGCATTGAGATGTTTATGTGTATGCATATCTAAAAGCACAGCACTTAATCCTTTACCTTGTCTATGATGCAAAGACCTTTGTTCACGTGTTTGTCTGCTGACCCTCTCCCCACNATTGTCTTGTGACCCTGACACATCCCCCTCTCCGAGAAACACCCACGAATGATCAATAAATACTAAGGGAACTCAGAGGCTGGCGGGATCCTCCATATGCTGAACGCTGGTTCCCCGGGTCCCCTTATTTCTTTCTCTATACTTTGTCTCTGTGTCTTTTTCTTTTCCAAGTCTCTCGTTCCACCTNACGAGAAACACCCACAGGTGTGGAGGGGCAACCCACCCCTTCA
|
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 |
|---|---|---|---|---|---|---|
| LTR5_Hs | SNAI2 | 939 | 946 | - | 13.45 | ACACCTGT |
| LTR5_Hs | GCM2 | 599 | 606 | + | 13.45 | ATGCGGGC |
| LTR5_Hs | esg | 939 | 945 | - | 13.41 | CACCTGT |
| LTR5_Hs | gcm | 599 | 605 | - | 13.38 | CCCGCAT |
| LTR5_Hs | POU2F1::SOX2 | 626 | 642 | - | 13.36 | CATAAACATCTCAATGC |
| LTR5_Hs | UGA3 | 820 | 826 | + | 13.34 | GGCGGGA |
| LTR5_Hs | cg | 34 | 44 | - | 13.31 | ACACAGACACA |
| LTR5_Hs | unc-86 | 644 | 651 | + | 13.31 | GTATGCAT |
| LTR5_Hs | PRDM1 | 869 | 875 | + | 13.28 | CTTTCTC |
| LTR5_Hs | SNAI3 | 939 | 947 | + | 13.25 | ACAGGTGTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
