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	ERF091	359	371	+	14.50	GTGGCGGAGGTGG
LTR85b	ERF9	44	62	-	14.38	GGAGGCAGAAGCGGCTGCA
LTR85b	ERF095	359	371	+	14.35	GTGGCGGAGGTGG
LTR85b	cg	475	485	+	14.17	CTACACACACA
LTR85b	ARF10	276	286	+	13.92	GAGGGGAGACA
LTR85b	TBX20	134	144	+	13.89	TGGGTGTGAAA
LTR85b	Tbox-a	135	143	+	13.81	GGGTGTGAA
LTR85b	RPN4	358	364	+	13.80	GGTGGCG
LTR85b	TBX3	135	143	+	13.80	GGGTGTGAA
LTR85b	sex-1	758	765	-	13.79	GAGGTCAC

1 2 3 4 5 6 7 ... 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).