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	POU2F2	290	302	-	15.88	ATATGCAAATGCA
LTR9B	POU2F3	151	159	+	15.87	TATGCAAAT
LTR9B	POU2F3	293	301	-	15.87	TATGCAAAT
LTR9B	POU2F3	382	390	+	15.87	TATGCAAAT
LTR9B	phol	186	195	-	15.85	CGCCATGTTG
LTR9B	POU3F4	151	159	+	15.57	TATGCAAAT
LTR9B	POU3F4	293	301	-	15.57	TATGCAAAT
LTR9B	POU3F4	382	390	+	15.57	TATGCAAAT
LTR9B	dl	111	120	-	15.57	GGGGCTTTCC
LTR9B	eor-1	476	488	-	15.56	AGAGACAGAGGGA

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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).