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	ZNF143	485	500	-	0.29	CTCACACAAGGCATTT
LTR85b	ZSCAN31	196	213	+	-0.77	GCTAAACTGCTCTGCATA
LTR85b	BPC6	2	22	-	-1.01	CAATTTTTTCCTCTCTGTTAC
LTR85b	Rarb	597	612	+	-2.79	TGAGATCGAGAGTTCA
LTR85b	NR1H2::RXRA	741	757	+	-3.34	AAATCTCAAAGGACAGG
LTR85b	BPC6	172	192	-	-3.55	CTCTTTGTTTCACTGTCTCCT
LTR85b	EWSR1-FLI1	509	526	+	-12.38	TGGGGAAATCAAGGAAAG
LTR85b	DAL81	571	589	+	-52.00	AACAGCCACGGGAGGTGAG

1 ... 44 45 46 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).