CR1-13_AMi

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0001291
TE superfamily	CR1
TE class	LINE
Species	Amniota
Length	724
Kimura value	35.73
Tau index	0.0000
Description	Non-LTR retrotransposon.
Comment	Fragment.
Sequence	AAAAAGGGATTAGAAAATAATACTGAANATANTATAATGCCATTATATAAATCGATGGTGCACTTCACTTGAATACCGCGTTCAGTTCTGGTCACCCTATCTCAAAGAAATANAGCAGAAATAAGGAGTTCGAGACGGGCGACGAAAATGATTAGAGGCAGAGAGACTTCCATATGAAGAGAGANTGAAGACTGGACTGTTTAGTTTAGAGAGGAGACGAATGAGGGGACATGATAGAGGTATACAAAATAATGAATGGACAGGGGAGCAATCGGGAGCTCCTATTTACCCTTTCTCATAATACAAGAACAAGGACATTCAATGAAATTGAAAGGCAACAATTTAAAACTGATAAAAGGAAATACTTTTTTTACACAATGCATAATTAACCTGTGGAACTCACTGCCACAAGATATCACTGAGGCCAAGAGCTTAGCAGGATTCAAAAAGGATTAGACATTTATATGGATAACGAGAACATCCGCAGTTACATTAGATAGGATAAAAAATATAAGGGATATAANCCTCATGCTTCAGGGCATAAGCCAACCACTAACTGACGGGGTTAGGAAGAAACTTCCCCTATGGGCAGGTTATTCCATAATTGCCATTATGGGGNTTTTGCACCTTCCTCTGAAGCATCTGGTACTGGCCACTGTCAGAGACAGGATACTGGACTAGATGGACCACTGGTCATTCCACTATNGCGAATTAATTGTTCTTA

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
CR1-13_AMi	LFY	681	699	-	17.65	GAATGACCAGTGGTCCATC
CR1-13_AMi	LFY	681	699	+	17.65	GATGGACCACTGGTCATTC
CR1-13_AMi	ZNF530	254	267	+	17.09	GAATGGACAGGGGA
CR1-13_AMi	MYB30	546	557	+	16.15	CCAACCACTAAC
CR1-13_AMi	eor-1	154	166	+	15.50	AGAGGCAGAGAGA
CR1-13_AMi	ZNF816	224	238	+	15.37	AGGGGACATGATAGA
CR1-13_AMi	POU4F1	379	390	+	15.16	TGCATAATTAAC
CR1-13_AMi	POU4F3	379	390	+	15.14	TGCATAATTAAC
CR1-13_AMi	AT1G19000	463	475	+	15.09	ATATGGATAACGA
CR1-13_AMi	SoxN	320	330	-	15.07	CAATTTCATTG

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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).