LTR1

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000375
TE superfamily	ERV1
TE class	LTR
Species	Haplorrhini
Length	783
Kimura value	9.46
Tau index	1.0000
Description	LTR1 (Long Terminal Repeat) for human endogenous retrovirus HUERS-P2
Comment	-
Sequence	TGATACGGGAGGGGGGCAGGGAAGTGCTGGGNAGAGAAGGGCGTGGTCCCTGGCTAGGGCTCCACCCCCGGGCCTGTGCCCACGGACCTAGGTGAGGACAGGCATTTCTGTTTTCGTGCCCAAATGTTGCATTTCCCAAGACCACCCTGGCCCGCCACGCCCCCATCCTGTGCCTATAAAAACCCCGAGACCCTAGCGGGCAGAGACACAAGNCGGCTGGACGTCGAGAGGAACACACCGGCGGAAGAGCACACCGACAGGCACCGGCAGACGCCGGCAGGCCATCGACCGGCGGAACGACGCGGAGTTTGGCCGGGGCGGTCGGAGGAGAGCCCGGCCGCTGAGCGGCCCGACTCCAGGGGAAAACCACCTTCCCACTCCATCCCCTTCTGGCTCCCCCATCTGCTGAGAGCTACTTCCACTCAATAAAACCTTGCACTCATTCTCCAAGCCCACGTGTGATCCGATTCTTCCGGTACACCAAGGCAAGAACCCCGGGATACAGAAAGCCCTCTGTCCTTGCGATAAGGCAGAGGGTCTAATTGAGCTGATTAACACAAGCCGCCTACGGACGGCTAAACTAAAAGAGCACNCTGTAACACACGCCCACTGGGGCTTCAGGAGCTGTAAACATTCACCCCTAGACGCTGCCGTGGGGTCGGAGCCCCACAACCTGCCCGTCTGCATGCTCCCCTAGAGGTTTGAGCAGCGGGGCACCGAAGAAGCGAGCCACACCCCCGTCGCACGCCCTGCGAGGGGGACAAGGGAACTTTTCCCGTTTCA

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
LTR1	E2FC	388	402	-	3.74	ATGGGGGAGCCAGAA
LTR1	IRF3	104	120	-	2.89	GGCACGAAAACAGAAAT
LTR1	TRP2	623	643	+	-0.42	AGCTGTAAACATTCACCCCTA
LTR1	EWSR1-FLI1	7	24	+	-1.59	GGGAGGGGGGCAGGGAAG
LTR1	EWSR1-FLI1	8	25	+	-4.32	GGAGGGGGGCAGGGAAGT
LTR1	TRP1	176	196	+	-5.17	ATAAAAACCCCGAGACCCTAG
LTR1	ZSCAN16	619	636	-	-19.62	GAATGTTTACAGCTCCTG
LTR1	BPC5	372	401	-	-48.50	TGGGGGAGCCAGAAGGGGATGGAGTGGGAA

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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).