LTR18B

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000429
TE superfamily	ERV3
TE class	LTR
Species	Primates
Length	614
Kimura value	10.99
Tau index	0.9287
Description	LTR18B (Long Terminal Repeat) for HERV18 endogenous retrovirus
Comment	LTR of HERVL endogenous retrovirus HERV18. 5 bp target site duplications. Not observed in other mammals.
Sequence	TGTAAGGTACATGGATGTGCTTTGGTCAAGGAATAGGCCGAGGCGGACATCCAGGCCTGCGTGACTCAGCGAGTTTGGNGCGCAGGCGCATANCTCCACTTGTTATATAACCTGTTTGTGTAAGNTCATACTTGGCTCTGAGCCACTATTGTCTGTAAAAGGTATAACTGCCCTGCTGACGCTGTACAGGGGCTCTTGGGGCTCGGCTCGGCTCAACATGGCTTGACATGGCGGGCGCGCTGGCGCCCAGAGAAAGAGAGAGAGAGCCAGAGCTGTCCGTCTTGCAGACGGACAGGGGGGAGCCAGGACACAGCTCGGCTCGCTCGTGCCCAGAGAGAGAAAGAGTTAAGCTGCTGACCCTGAAGGCAAGGGAGAGCCGGCCGCGCAGCTGTGCGTGGGGGCGGCAGGAGCCGCAGAGCCGGANCAAGCAGCCGAGACAGAGGCGGACAGTGTGAGAGAGCTGCTGAAGTGTGAGAAGCTGCTGATGAGAGAGCTGCTGAATAAAACCATATTTCACCTGCCTACGGCCCCCCGAGTGTTCTTTCAGCTATCTGCCCATCCACCCACTCCCCTCGGACCTCAGCATGGGCTGGAACCTGACCCCGGGCCTGACA

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
LTR18B	BPC1	248	271	+	25.68	CAGAGAAAGAGAGAGAGAGCCAGA
LTR18B	BPC6	252	272	-	25.37	CTCTGGCTCTCTCTCTCTTTC
LTR18B	ZSCAN31	162	179	+	24.19	GTATAACTGCCCTGCTGA
LTR18B	BPC6	250	270	-	23.86	CTGGCTCTCTCTCTCTTTCTC
LTR18B	RAMOSA1	252	265	+	22.33	GAAAGAGAGAGAGA
LTR18B	RAMOSA1	250	263	+	19.36	GAGAAAGAGAGAGA
LTR18B	RAMOSA1	254	267	+	18.71	AAGAGAGAGAGAGC
LTR18B	Nrf1	80	91	-	18.54	ATGCGCCTGCGC
LTR18B	eor-1	249	261	+	17.79	AGAGAAAGAGAGA
LTR18B	NFIC::TLX1	132	145	-	16.49	TGGCTCAGAGCCAA

1 2 3 4 ... 42

Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.

The promoter activity across 46 body sites from The Genotype-Tissue Expression (GTEx) project.

The promoter activity across 33 cancer types from The Cancer Genome Atlas (TCGA).