LTR85b

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000604
TE superfamily	Gypsy
TE class	LTR
Species	Eutheria
Length	784
Kimura value	33.12
Tau index	0.9939
Description	LTR85b (Long Terminal Repeat) with unclear association (possibly Gypsy)
Comment	4 bp TSDs.
Sequence	TGTAACAGAGAGGAAAAAATTGCTATTTAAAACCANAACTGACTGCAGCCGCTTCTGCCTCCTAAGGGAGTGGCANAATTCCTCTCCGGAGNAGATGGCTCTTTGTTTAGGAAAATACCTTGATAGGCCNCTTTGGGTGTGAAAGGTGAGGCCCCCAGGGCATGGTCTGGAAGGAGACAGTGAAACAAAGAGANAGCTAAACTGCTCTGCATAANAAAATGAACAGAATTTNGGGGANNTGGAGGGNNGGNAGGAGAGGGGAGAGGGAGNTGAGAGAGGGGAGACAGGGGCAAGCAACTGAGAGAAGTCAGGAGATATGGGAAGCCTGTGGAGAAAGGTGGCCAGTGAGAAATTCCCGGTGGCGGAGGTGGCCGAAGGACTTTTAAGAACAGGGATGTCTAATATTCAATTTTAAGTTGTTTGCGTTGCTGTGATGTAACCCCCTCCGTCNCCCCAAACCTTCAGTAAAGTCTGCTACACACACAAATGCCTTGTGTGAGTGGTGTTTTGGGGAAATCAAGGAAAGGGGCTGNGTTCCACGTCTGGGTCGGCGCGGAGCAGAGAGAAGAGAACAGCCACGGGAGGTGAGACGCGAGTGAGATCGAGAGTTCAGCGGAAGCAGGAANTCGGAGCCAGAGGTGACCATGAGAACGTAAGCCCCCCGGGAATTCGCAGAAATCTTGGGGAGGGCATTGGACTTCCCACAGGATGTGGGATGGGGGTTTGAGCCAATTTTATTTAAATCTCAAAGGACAGGGTGACCTCAGCTGACATCTGGGTTACA

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
LTR85b	TFAP2B	152	162	+	15.02	CCCCCAGGGCA
LTR85b	Fer1	761	773	+	14.98	ACCTCAGCTGACA
LTR85b	Tbx6	135	143	+	14.98	GGGTGTGAA
LTR85b	ERF014	357	371	-	14.95	CCACCTCCGCCACCG
LTR85b	TFAP2C	152	162	+	14.83	CCCCCAGGGCA
LTR85b	ERF2	356	368	-	14.65	CCTCCGCCACCGG
LTR85b	NAC69	488	495	-	14.59	ACAAGGCA
LTR85b	ERF077	359	368	-	14.58	CCTCCGCCAC
LTR85b	ZNF341	570	577	+	14.55	GAACAGCC
LTR85b	TWIST1	771	778	-	14.54	CCAGATGT

1 2 3 4 5 6 ... 47

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).