LTR7C

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000588
TE superfamily	ERV1
TE order	LTR
Species	Catarrhini
Length	470
Kimura value	10.47
Tau index	0.9171
Description	Long terminal repeat of an HERVH endogenous retrovirus
Comment	LTR of an HERVH element active 25-40 MYA. At least 3 distinct subfamilies in this set, but each with very few copies.
Sequence	TGTCAGGCCTCTGAGCCGAAGCTCAGCCATTGTAACCCCTGTGACCTGCACATATACGTCCAGATGGCCTGCAGGAGCCAAGAAGTCTGGAGCAGCCGAAAAACCACAAAAGAAGTGAAACAGCCAGTTCCTGCCTTAACTGATTAACCAACCTTACGACATTCCACCATTGTGACTTGTCCCTGCCCTACCCCAACTGATCAATCGACCTTGTGACATTCTTCTTCTGGACAATGAGTCTTATGATCTCCCCACCATGCACCTTGTGACCCCCTCCTCTGCTGACAATAGATAACCACCTTTNACTGTAACTTTCCACTGCCTACCCAAGTCCTATAAAGCNGCCCCTCCCCTATCTCCCTTCGCTGACTCTCTTTTCGGACTCAGCCCACTTGCACCCAAGTGAATAAACAGCCTTGTTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGCTTGACA

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
LTR7C	RUNX2	101	109	+	13.37	AAACCACAA
LTR7C	NEUROD1	60	67	+	13.36	CCAGATGG
LTR7C	MYB58	437	445	-	13.35	CCACCAAAC
LTR7C	Atoh1	61	67	+	13.34	CAGATGG
LTR7C	NDT80	103	111	+	13.33	ACCACAAAA
LTR7C	Spps	344	354	+	13.33	GCCCCTCCCCT
LTR7C	NEUROG2	61	67	+	13.29	CAGATGG
LTR7C	TEAD1	159	167	+	13.28	ACATTCCAC
LTR7C	TEAD3	159	166	+	13.20	ACATTCCA
LTR7C	KLF1	345	352	-	13.17	GGGAGGGG

1 2 3 4 5 6 7 ... 19

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).