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 | Yy1 | 69 | 76 | - | 14.43 | CAAAATGG |
| LTR5_Hs | TFAP2B | 576 | 586 | - | 14.40 | GCCCTAAGGCG |
| LTR5_Hs | Ptf1A | 939 | 946 | - | 14.30 | ACACCTGT |
| LTR5_Hs | GCM1 | 599 | 608 | + | 14.30 | ATGCGGGCAG |
| LTR5_Hs | AT3G10030 | 111 | 118 | - | 14.25 | TTAACAGA |
| LTR5_Hs | vnd | 266 | 274 | + | 14.22 | TCTCAAGTA |
| LTR5_Hs | snai-1 | 939 | 945 | - | 14.14 | CACCTGT |
| LTR5_Hs | unc-86 | 646 | 653 | - | 14.03 | ATATGCAT |
| LTR5_Hs | DOF5.8 | 887 | 905 | + | 14.02 | TCTGTGTCTTTTTCTTTTC |
| LTR5_Hs | Hmx2 | 663 | 677 | + | 13.87 | CAGCACTTAATCCTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
