HERV16
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000162 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Theria_mammals |
| Length | 4996 |
| Kimura value | 32.10 |
| Tau index | 0.9660 |
| Description | ERVL endogenous retrovirus, HERV16 subfamily (internal) |
| Comment | LTRs of HERV16 are listed in Repbase as LTR16 sequences. HERV16 is related to HERVL and is relatively old (>20% divergence from consensus). Bases 300 to 1300 encoded a GAG protein closely similar to the murine "retrovirus restriction polypeptide" (PIDs e24674 and e242676). |
| Sequence |
GTTGGTACCAGGAGTGGTCCGAGAAAGCAGACGNTNCTAAGATGGGATTTTGGAGCTGGATCACCCGCCGNCCGGCTGGCAATGAGGACCCCATCACTGGTGGTAGGTGGAGCACGGATAGCCCCTGGCACGAGGTAGCGGTGCAATTGTTAAAACTTTCACCGGTGGTGAACTGGGATGGNATACCGGTGGAAAGAGAATGCACTGGCNGGTGCAATGTNTCAGGCGTTTGAGAAATATGGGANGAATTAANTACATGNAAGGACAATGGAATTGGATGGCTGTTGCTAAGCNCGACTGACGCTCTGGAAAAAGACAATGAAAGGCTGAGAGCGATTAATCGNCAATTNAAAGCTAAGTGTGAAAGCCAGAGGGCCTCCTTGGCAGCATATAAAGAGACTCTCATCTCCTGCAGCCGGAGGGCAGAGAAAGCTGAGGATCAGGCCCAGGACTTAATCAGAGTAGCAGAGCTCCAGAGAAGGTTGAATTCTCAACCNAGGCAGGTCTGCTATGCCAAGGTCAGGGCCCTGGTTGGGAAAGAATGGGACCCTGANACNTGGGATGGGGACATCTGGGTCGATGCNCCTGAAAATCTTGAATCCCCAGATTCCCCTGAACCCTCTGGGCCTGCAGAAGTGGCCCACTCCTCCCTGTTAAGGGCTAGCACTCNCTCCTTGCTTCGCGNGAAGACGATGCAGAGGCCTCTNCCTTNGCAAGACAACATGCGCCCCCCTCAGGATCTGCCCCCACCTCCCCTCCTGGCCACCAGACCAATAACTAGGGTTAAGTCACAGCATAACCCGGCCGGGGAAGTGCTGGGCCTGNTAAGGGAGGAAAGGGACTATACCCCAAAGGAGCTGCAGGACNCGNCTAGCCAGCATGTACCGGCAGGACCGGGAGAGTACGCATGGGACTGGATTCTGAGGGTGCTGGATCAAGGGGGNCGGAACATAAAGTTGGATAAGGGAGAGTTTATCGATNTGGGAGCACTCTCCCGNGATACAGGATTTAACACCCTGGCAAGGACCCCGGGAGATGGTGCNAACACGCTGCTAGGATGGCTCCTGGAAGCNTGGAGAAAGCGATGGCCCACACTAAGTGAAGTAGAAATGCCAGAACTGCCGTGGCAGACGGTGGAAGAAGGGATCAAAAGGCTCAGAGAAGTGGGCATGCTAGAGTGGATATACTATGTAAGGCCGGAAAACCCACCAGATGACTATGTTCCGCGGGAGGGCCCAGAGGACACNCCATTTACCAAAGCNATAAGGAATGCGCTGGTGAGAGGGGCACCAGCATCACTGAGAAGCTCAGTGGTGGCTNTCCTCTGCAGGCCAGGGCTGACGGTAGGAGANGCCGTTACAGAACTGGGCTCNCTGATAGCAATGGGGATGATAGGACCCCGAAATAATAGAGGCCAGGTGGCGGCGCTTAACCGTCAGAAGCAAGGTGGGCGCAATTATCGTAATGNACGGCAAGGTCGGAGTGGCAGCCGGGGGGGCCTGACCCGCAGAGAGCTATGGAGATGGTTAATAGAACACGGCGTCCCTAGGGGCAAGATAGATGGGCAGCCAACAGGAAGNCATGGACAGTTAATAGAACATGGCGTCCTAGGGGCAAGATAGATGGGCAGCCAACAAGGGTGTATTGCTCAACTNAAACAANCAAAAGAAATCAAGGATGGATGANCAGGAGGCTGAGGGCAGTCGCCCCAATAAAAAGTCACGATCCCTTGCCCAGTTTCCGGACCTGAGCCAGTTTTCAGACCCGGAACCCATTGACTGAAGGAGAGGCCGGGTCCCCAGGAGGAAGGACCCTGCAACACCACGGCAAGTGTACACGGTAATGATTCCCCCAGTCCTTCCCCAAAGGGACCTACGGCCATTTACTCTGGGTAACCGTACACTGGGGAAAGGGGAATACCCAGACATTTCGAGGACTGTTGGACACAGGGTCCGAGTTGACATTGATACCCGGAGACCCGAAGCGTCATCATGGCCCTCCCGTTAGAGTGGGGGCATATGGGGGCCAGGTAATAAATGGAGTCCTGGCCCAGGTCCGGCTCACAGTGGGTCCACTGGGTCCACGGACCCACAGTGGTCATTTCCCCGGTCCCCGAATGTATAATTGGAATGGACATACTTGGTAGTTGGCANAACCCCCACATTGGTTCCTTGGCCTGTGGGGTAAGAGCTATCATAGTGGGGAAGGCCAAGTGGAAGCCTCTGAAACTGCCCTCACCTTCTCCGGNCAAGATAGTAAATCAAAAACAATATCGCATCCTCGGGGTGGAGAATGGCAGAGATTAGTGCCACCCTTAAAGACCTAAAGGATGCAGGAGNTGTGGTCCCCATCATATCTCCATTTAATTCACCAGTNCNGGCCCCTGCAAAAACCAGACGGATCCTGGANGACGACAGTGGACTACCGCAAACTCAACCAAGTAGTANCCCAATTGCAGCTGCTGTGCCAGATGTGGTATCTTTGCTAGAGCAGATTAACACGGCCTCAGGTACGTGGTATGCGGCCATTGATCTGGCGAATGCGTTCTTTTCCATCCCTATCAGAAAGGAGGATCAGAAGCAGTTCGCATTCACNTGGAACGGACAACAGTATACATTTACAGTCTTGCCCCAGGGCTNTGTTAACTCTCCTGCCCTCTGTCATAATATAGTCCGAAGGGACCTGGACCATCTGGACATTCCGCAGAACATCACATTGGTCCACTATATCGATGACATCATGCTAATCGGACCGGAATGAGCAAGAAGTGGCAAGTACGTTGGAGGCCTTGGTAAGACACATGCGCTCCAGAGGGTGGGAGATAAACCCTACGAAGATTCAGGGGCCTGCCACATCAGTGAAGTTTTTAGGGGTCCAGTGGTCTGGGGCATGCCGGGACATCCCCCCAAAGTAAAGGACAAATTATTGCATCTTGCACCTCCCACCACNAAGAAGGAAGCACAACGCCTGGTAGGCCTCTTCGGGTTCTGGAGGCAGCATATTCCACACTTGGGAATACTGCTCCGACCCATNTACCGGGTGACGCGAAAGGCTGCCAGCTTTGAGTGGGGCCCAAGCAGGAAAGGGCTCTGTAGCTNACCGCATATCGTGTNCGAANCGCANANNCGGNCCTCCAAGTCATAAAGTNGGGCGGGCCCAGCAGCAGTCCATCATAAGGTGGAAATAGNATATCCGAGATTAAGCCCGAGNAGGACCAGAGGGCGCAGGTNAGNTNCATGAGCAGGTAGCCCAGACCCCCATGNCACCCACCACNGTTGCACCAGCGCCTCTCCTTCGGCTCGCACCTATGGCCATATNGAGGNNTGTGGTCCCGTATGACCAGCTGAAGGAAAGCTCGAGCTTGGTTTACAGGATCAGCTCGGTATGTGGGCGCAAGCCAAAATANGTGGTGGCTGCACTACAGCCCCATTCAGGGGTGGCCCTGAAAGGCAGCAGGGAGTGAAAATATCTTCCCAGTGGGCAGAGCTGCGAGCAGTGCACCTGGTCATCCACTTTNCGTGGAAGGAGAAGTGGCCCGAGATGGTAATATATACGGATTNCTGGACAGTGGCCAATGGCCTGGTCGGCTGGTCAGGAGCTTGGAAGGAAAAGATTAGAGANAGGGAAGTCTGGGGTAGAGGCATGTGGATAGACATATNGGAAGTGGCACGAAATACGAAGATTTTTGTATCGNTNNTATGTTAACGCTCACANGAAAGCATCNACCATGAAAGAGNCACTGAACAACCAAGTAGACAAAGTGACTTCGACCACTGACGTTAGCCAGCCTTCGTCCCGGCCTCCTCAGANCTGGTNCAACGGACATCTCAANAAAGTAGCCATGGTGGCAGAGATGGAGGCTACGCATGGGCCCAACAGCATGGACTCCTATNCACCAAGNCGATCTAGCTGCTGCCCCGTNTGAATGTCCAACCTGCAGCAACAGAGACCAATGCTCTACCTCNAATACGGCACTATTTATGGAGACCACTTAGCGGCGAATTGACTATATTGGACGCCTTCCATCCTGGAANGGNCAGNGATTCATTCTCACAGGAATANATACNTATTCCGGGTATGGGTTTGCCTTTCCTGCCTGCANAGCCTCATCNAGCATCTGAGGGNCTTAGGAGTGCCTGATCCACAGGCATGGAATCCCACACAACATAGCATCTGANCAGGGCGCTCACTTCACAGCAAAGAAGNGGCACAAGTGGGTCCANAATAACGGGATCCACTTATCNTATCACGTACCGCACCATCCAGAAGNAGCTGACCTNATAGAACGCTTCTGAAGGCACAGNTGAAGCACCAGTNGAGGCGAACTCTGAAAGAATTGGGTGCCATCCTCCAGGATGCAGTATATACATTGAATCANAGGCCTATNCGTNGGGCNTTGNNTCTAATNGGGAGAATGGGATTAGGAATAAGAGGTGAAAGCAGGAGTGTGCCTACTCCCCATCGTAGTGGCCCACAAGGATCACAGCAGTGGTTTGAACACGGATTGGACTACTGATATCCAGGAATCGCCGCACAAGAAGGNGAATCCACATTTGGCAGGAGTAATTGACCNTGATCANCAGGAGGGGTAGGGCTGCTNTCGCANAATGAGGAAGAAAGGAATATGTNTGGAACCAGGTGATCCNCTTGGGTGCCTCCTGGTACTCCCTTGCCCCATTTAACTGTAAATGGACAATNCCACCGAAAAGAGCTCGGACCNCTCCGGAATGAAGGTTTGGNTCACATCGCCNGGTAAGCCACCAAGACCTGTCGAAGTGATAGCTGNGTGAGGGANATCTAGAATGGATAGTAGAAGAGGGAGACGATGAGTACCAGTTNCGGCCCCGAGACCAACTGCAGCAANNGGGGCTGTAGTTCGTCCCACTAACCTCCCTCTTCTAAGTTTCGCTTCAGAAAGAGAAGCTTAAAGGAATAATGGAGGAACTGCTCCNNGAACCTGNGTGGAGAAGTAGATCCGTCGAGTACAAAGGTGGAC
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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 |
|---|---|---|---|---|---|---|
| HERV16 | RVE4 | 3463 | 3471 | - | 16.53 | AGATATTTT |
| HERV16 | ARALYDRAFT_897773 | 2341 | 2349 | - | 16.39 | GGGGACCAC |
| HERV16 | RVE7 | 3463 | 3471 | + | 16.38 | AAAATATCT |
| HERV16 | ERF076 | 1419 | 1428 | - | 16.36 | GCGCCGCCAC |
| HERV16 | SoxN | 266 | 276 | - | 16.34 | CAATTCCATTG |
| HERV16 | CRF4 | 1419 | 1428 | - | 16.34 | GCGCCGCCAC |
| HERV16 | ATF2 | 2732 | 2741 | - | 16.33 | ATGATGTCAT |
| HERV16 | NFKB2 | 1912 | 1922 | - | 16.30 | GGGTATTCCCC |
| HERV16 | TCP7 | 3066 | 3076 | + | 16.26 | GTGGGGCCCAA |
| HERV16 | GT-4 | 775 | 786 | + | 16.24 | TAACTAGGGTTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
