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	E2FC	489	503	+	16.41	AGTGTGCCGCCAAAA
Charlie31a	lsy-2	417	424	-	15.13	CTACAGTA
Charlie31a	FOXP2	316	324	+	14.61	AGTAAACAG
Charlie31a	bHLH80	189	197	-	14.56	AGCAAGTTG
Charlie31a	ZNF417	236	242	+	14.55	GGCGCCA
Charlie31a	IG1	492	500	+	14.40	GTGCCGCCA
Charlie31a	IG1	59	67	+	14.40	GTGCCGCCA
Charlie31a	Ptf1A	53	60	-	14.30	ACACCTGT
Charlie31a	bHLH130	189	196	+	14.26	CAACTTGC
Charlie31a	daf-16	255	262	-	14.26	GTAAACAC

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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).