FordPrefect_a

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0000146
TE superfamily	Tip100
TE class	DNA
Species	Eutheria
Length	508
Kimura value	25.22
Tau index	0.0000
Description	hAT-Tip100 DNA transposon, FordPrefect_a subfamily (non-autonomous)
Comment	FordPrefect_a is an internal deletion product of FordPrefect. It had (at least) 41 CpG dimers, basically representing a mobile CpG island.
Sequence	CAGTACCGCCCTTAGACCCGGGCAAGCGGGGCCCCTGCCCCGGGCCCCGCGCCTCAGGGGACCCCGCGCTTTGGAGTGCCTTCCTCGAAATTTTCTAAGTCCCCCTCCGGTGCCTGGGACCGGCCGGGGCCGGCAGTGCCATCCGGGCGGGGCGCCCCGAGCCCGGACCGGGACCCGCGTGGGCCCCGGTCCCCGTTTCTCCCCTTCGGGGCGCTCTCCGACCCTCTACCCCATGCGTGGGGTCGACCAGATGCCCCGAGGAGCTCCGGGACTCGCGCCTATGGGGTCGTCCCGGGGCCCCGTGGCCGGGCCCCGGTTCCAGGAGGGCGGCCTGGCGAGCGGATCGCTCCCGCTGGCCGGCGCGGTATTTCTTTCGCGGGATCGCGTGAGATTGGGCCGCCAGAATGGTGCTGACACGCTGATTTNGGGTGACTCAAATTGTTTATATAGACAGGGGCCCCGCAAAAAATATTTGCCCGGGGCCCCGCACACCCTAGGGGCGGCCCTG

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
FordPrefect_a	BAD1	477	488	+	19.90	CCGGGGCCCCGC
FordPrefect_a	BAD1	305	316	-	19.20	CCGGGGCCCGGC
FordPrefect_a	BAD1	39	50	+	18.56	CCCGGGCCCCGC
FordPrefect_a	BAD1	306	317	+	17.20	CCGGGCCCCGGT
FordPrefect_a	BAD1	292	303	+	16.72	CCGGGGCCCCGT
FordPrefect_a	PATZ1	143	153	+	16.65	CCGGGCGGGGC
FordPrefect_a	FOXE1	439	450	-	16.52	CTATATAAACAA
FordPrefect_a	TCP23	179	186	-	16.36	GGGCCCAC
FordPrefect_a	KLF15	145	152	-	16.27	CCCCGCCC
FordPrefect_a	cassava45561.m1	179	187	-	16.09	GGGGCCCAC

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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).