LTR17

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000427
TE superfamily	ERV1
TE class	LTR
Species	Catarrhini
Length	780
Kimura value	4.64
Tau index	0.9806
Description	LTR17 (Long Terminal Repeat) for HERV17 endogenous retrovirus
Comment	LTR17/HERV17 elements are flanked by 4 bp direct repeats.
Sequence	TGAGAGACAGGACTAGCTGGATTTCCTAGGCCGACTAAGAATCCCTAAGCCTAGCTGGGAAGGTGACCGCATCCACCTTTAAACACGGGGCTTGCAACTTAGCTCACACCCGACCAATCAGGTAGTAAAGAGAGCTCACTAAAATGCTAATTAGGCAAAAACAGGAGGTAAAGAAATAGCCAATCATCTATCGCCTGAGAGCACAGCGGGAGGGACAATGATCGGGATATAAACCCAGGCATTCGAGCCGGCAACGGCNACCCCCTTTGGGTCCCCTCCCTTTGTATGGGAGCTCTGTTTTCACTCTATTAAATCTTGCAACTGCACTCTTCTGGTCCGTGTTTGTTACGGCTCGAGCTGAGCTTTCGCTCGCCGTCCACCACTGCTGTTTGCCGCCGTCGCAGACCCGCCGCTGACTTCCATCCCTCCGGATCCGGCAGGGTGTCCGCTGTGCTCCTGATCCAGCGAGGCGCCCATTGCCGCTCCCGATCGGGCTAAAGGCTTGCCATTGTTCCTGCACGGCTAAGTGCCCGGGTTCGTCCTAATCGAGCTGAACACTAGTCACTGGGTTCCACGGTTCTCTTCCGTGACCCACGGCTTCTAATAGAGCTATAACACTCACCGCATGGCCCAAGATTCCATTCCTTGGAATCCGTGAGGCCAAGAACCCCAGGTCAGAGAACACGAGGCTTGCCACCATCTTGGAAGCGGCCCGCCGCCATTTTGGAAGCGGCCCGCCACCATCTTGGGAGCTCTGGGAGCAAGGACCCCCCGGTAACA

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
LTR17	ERF4	713	721	+	16.16	CCGCCGCCA
LTR17	ERF077	713	722	+	16.14	CCGCCGCCAT
LTR17	PLT1	644	659	-	16.12	CTCACGGATTCCAAGG
LTR17	ERF112	713	721	+	16.11	CCGCCGCCA
LTR17	MAZ	273	280	+	16.08	CCCCTCCC
LTR17	REF6	293	301	-	15.93	AAAACAGAG
LTR17	POU1F1	141	154	-	15.69	CTAATTAGCATTTT
LTR17	ZIC1	202	215	-	15.64	TCCCTCCCGCTGTG
LTR17	ERF118	713	720	+	15.56	CCGCCGCC
LTR17	IG1	713	721	+	15.50	CCGCCGCCA

1 2 3 4 5 ... 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).