LTR9B

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000623
TE superfamily	ERV1
TE class	LTR
Species	Haplorrhini
Length	644
Kimura value	9.68
Tau index	0.9765
Description	LTR9B (Long Terminal Repeat) for ERV1 endogenous retrovirus
Comment	LTR9B is similar to LTR9 over its full length and is found flanking closely related internal sequences (mostly HUERS-P3b). 4 bp TSDs. HUERS-P3 LTR.
Sequence	TGTTGTAGGAGTTATTAAGAAATTATTTTAGGCAGATAGAGAGGAAAAGGGGTCCTTGGGAAGTTTTCGTTTCTTTTTAAAGCAGCTCCAGAAACGTTTCTTGTCTAGCAGGAAAGCCCCGGCTCTTAGAGCCGGGCCGGCAACCTTTGATATGCAAATGCAGGCCATTAGAAACTGGGTCCACCCAACATGGCGATTCCCGCCGTCGTCTTCTTGCCCTTGCCCCACATGTGCCTGGCAACATGGCCGCCCCCACATATCCCCACGTGTGTAGAACATCATGGCGCCCTGCATTTGCATATTAAAAGGCTAGGGTGGGAGGGCCAGTTTTTTCGCGGGCTACGTGAATGACATGCCTGGTCAAACCAATCCCCTGAGCCCTATGCAAATCAGACACCGCCTCCTCCAGCCTCCTCATATAACTGGCTGGTNTCCGCCGCACNCGGGGTTTCCTCTCTCGGCTTTGGAGCCCCCCTCCCTCTGTCTCTGTACGGGGGAGCTTCTTCCTTCTTTCTTCTCCCTTCTTTCTTGCCTATTAAACTCTCCGCTCCTTAAAACCACTCCACGTGTGTCCGTGTCGTTTTATCTAANTCGGCGCGAGGACCAAGAACCCTGGTGTTCCTCCACTCATCGGAGCCGTATCA

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
LTR9B	nub	151	161	+	15.55	TATGCAAATGC
LTR9B	nub	291	301	-	15.55	TATGCAAATGC
LTR9B	RELA	111	120	-	15.52	GGGGCTTTCC
LTR9B	POU1F1	290	303	+	15.51	TGCATTTGCATATT
LTR9B	TCP16	177	184	-	15.32	GTGGACCC
LTR9B	POU2F2	381	393	+	15.31	CTATGCAAATCAG
LTR9B	E2F6	197	204	-	15.29	GGCGGGAA
LTR9B	PATZ1	471	481	-	15.22	GAGGGAGGGGG
LTR9B	REL	111	120	-	15.13	GGGGCTTTCC
LTR9B	Wt1	247	256	+	15.11	CCGCCCCCAC

1 2 3 4 5 6 ... 54

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).