Charlie31a

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0001244
TE superfamily	Charlie
TE class	DNA
Species	Eutheria
Length	554
Kimura value	31.04
Tau index	0.9730
Description	hAT-Charlie DNA transposon, Charlie31a subfamily
Comment	8 bp TSDs with NNCTAGNN preference. Terminal 80-90 bp similar to those of autonomous Charlies (like Chaplin6_FR and Charlie17), on which the orientation is based. Present in elephant, sloth, human, absent in marsupials.
Sequence	CAGTGGTTCTCAACCGGTGTGCCGCGGCACACCGGTGTACCGCGAACCCTTCACAGGTGTGCCGCCAAATTTTGATCAATGTGTAAAATTTATTTTTGCTACAACTGAGTATACATACTGTTACGGCGATGTCTGTCAGACGGAACGTTGAGCTGAGCGGGTCGTGCGACGCGGTGTAGAGCGGGGTACAACTTGCTGCGAGTAAGAGGTAAGAGGCATAGCGTAACGTCAAGCCGGCGCCAAAGAAAGATCGCGTGTTTACTGGAACATGCGAGAACTTTGCCTCGTGAGTATATAAGAGAGCGCGGTCAGGGCAGTAAACAGTTCTACTCAAACAGCGACACAGTGCTGAAGGGCGACCAAGTGAATAGTGCGATAACTGTGGATGCTTTTATAGACACTGTGAGACATTGTTATACTGTAGTAGTGATTGCGTTGTAATTATTGCTGACTTGTTTAGTGTTGTTTTGAGTCTTTTAATCCCTTCAAGTGTGCCGCCAAAAATTCTAGTATTCGAAAGTGTGCCGCGAACACAAAAAGGTTGAGAACCACTG

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
Charlie31a	brk	234	241	+	13.31	CCGGCGCC
Charlie31a	GRF6	134	140	-	13.30	TCTGACA
Charlie31a	Mafb	442	452	+	13.29	TTATTGCTGAC
Charlie31a	SNAI3	53	61	+	13.25	ACAGGTGTG
Charlie31a	Nkx2-1	486	492	-	13.15	CACTTGA
Charlie31a	DOF4.2	535	545	+	13.12	AAAAAGGTTGA
Charlie31a	ZHD3	439	447	+	13.12	TAATTATTG
Charlie31a	JUB1	123	129	+	13.11	ACGGCGA
Charlie31a	BHLH122	189	195	+	13.03	CAACTTG
Charlie31a	GRF9	134	140	+	13.03	TGTCAGA

1 2 3 4 5 6 7 ... 23

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).