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	PITX2	477	484	+	13.60	TTAATCCC
Charlie31a	ATHB-40	439	449	-	13.59	AGCAATAATTA
Charlie31a	ATHB-13	440	447	-	13.57	CAATAATT
Charlie31a	SNAI2	53	60	-	13.45	ACACCTGT
Charlie31a	FKH2	256	262	-	13.43	GTAAACA
Charlie31a	FKH2	317	323	+	13.43	GTAAACA
Charlie31a	esg	53	59	-	13.41	CACCTGT
Charlie31a	ATHB-51	440	447	+	13.40	AATTATTG
Charlie31a	CUP2	91	101	-	13.33	TAGCAAAAATA
Charlie31a	Trl	297	305	+	13.33	AAGAGAGCG

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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).