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	Os05g0497200	235	242	+	14.24	CGGCGCCA
Charlie31a	HSF4	265	277	-	14.17	TTCTCGCATGTTC
Charlie31a	snai-1	53	59	-	14.14	CACCTGT
Charlie31a	tj	443	452	-	14.13	GTCAGCAATA
Charlie31a	ATHB-20	440	447	-	14.11	CAATAATT
Charlie31a	ATHB-53	439	447	-	14.03	CAATAATTA
Charlie31a	Hsf1-2-4	265	282	-	13.98	CAAAGTTCTCGCATGTTC
Charlie31a	ZNF257	206	215	+	13.92	GAGGTAAGAG
Charlie31a	FOXP2	255	263	-	13.68	AGTAAACAC
Charlie31a	NRL	442	453	+	13.66	TTATTGCTGACT

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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).