Charlie29b

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0001176
TE superfamily	Charlie
TE class	DNA
Species	Eutheria
Length	1194
Kimura value	27.74
Tau index	0.0000
Description	hAT-Charlie DNA transposon, Charlie29b subfamily
Comment	ORF remnant from 467-955 encodes the C-term of a transposase with consensus 49% identical (66% similar) to Charlie25_tp in mammals, hAT-1_MEu in marsupials, and Chaplin5_FR_tp in Fugu. Positions 1-467 and 913-1194 comprise the previously described subfamily Charlie29a. Present at orthologous sites throughout Eutheria, but not in marsupials.
Sequence	CAGTGTTTCTCAAACTGGGGTCCGCGGACGTATTCTCGGGGGTCCGCGAGTTCTCTACGAGAATTTTTNAATTTTGTGTTTTCATTTCGATGATAATCTAAAAAAATTAATATAAGCATATTCTGGATCATCTGGATGACCACCTTATAACCGAGTACTGCCACGCGATTTCAGTGCCCGCGTTTGCGTTTGTGTTTACGATCGCGTTGGCGCCAAGTAGTACTACTTTAATTGTCGCGGGCTAATGAGAAAAGAACAGAGGCGGACTTAATACGTAAATGATGCGTTCGCGCCAAGTGAAGGCCAAATGACGTCACGGCGCGCTGTACGAACGAAGGTTTCGCAGTAGTTCGAATAGAGAAAAGTGGTGGGAGAATTGAGTCATCACACGGCACACGGTAGTATAGGCATGCCGAACTCAAAAGAACCTGCGCCGTAGCAGTCAGTACCATATTCACGTTGCGAGCAGATGTATTGCGCGGATCCCGTCTTTGTACGTACCAACTTGCAACAGTTCATTAGCAGTAAGTGTAGTAGTAAATACGCAATGAAGAATTTTTCTGTTCCCGATTCCAGCAATAATTGGATTAGATACCCATTTAATGCAGATTTCAATAACGCCGCAATGCTAACCTTATCTTCAAGTGAACAAGACAGCTTTACAGAGTTATCAAGTGACACCTCATTAAAATTGGCATTCGAGGATTGCTCGCTGGCAGAGTTTTGGTTAAGTATGAGGTCTGATTATCCTGAACTAGCAAACAAAGCCTTGAAGTTATTAATACCATTTTGTACAACATACTTATGCGAACAGGCATTCTCTGCATTAGTATTATTGAAGTCAAAATACAGAAACAGATTAAATATAGAACCGGACCTGAGGCTACATCTTTCTACTATTAAACCCAACATCGGCGATTTAGTTTCAGCAAAACAACATCATCCGTCACATTAAATTAATGTTGTTAATTTGAATTTTATTGGTTTTGTAGTTTTGTTTGTATTTAATTTGTAAATTTGTTTTGGTTTTATAGTTGTATAAGAGCTATAAGCATAAGGAGTTTATACCTAGTTTTATGTTTGTACATATTTAAGTAACATTATAATAAAAATAATTTAAGTCAACACTGGGGGTCCGCGAGAATTTTTTTCCTTAAAAGGGGTCCGTACATTACTCAAGTTTGAGAAACACTG

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
Charlie29b	JDP2	308	317	+	18.60	ATGACGTCAC
Charlie29b	Creb5	308	317	+	18.09	ATGACGTCAC
Charlie29b	TCX3	967	978	-	17.89	AAATTCAAATTA
Charlie29b	ATF3	308	317	-	17.83	GTGACGTCAT
Charlie29b	ATF3	308	317	+	17.81	ATGACGTCAC
Charlie29b	JUNB	308	318	+	17.57	ATGACGTCACG
Charlie29b	Creb1	308	317	+	17.53	ATGACGTCAC
Charlie29b	Creb1	308	317	-	17.53	GTGACGTCAT
Charlie29b	ATF7	308	317	+	17.53	ATGACGTCAC
Charlie29b	TGA2	308	317	+	17.05	ATGACGTCAC

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TFBS enrichment in GRCh38

Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.

GTEx

The promoter activity across 46 body sites from The Genotype-Tissue Expression (GTEx) project.

TCGA

The promoter activity across 33 cancer types from The Cancer Genome Atlas (TCGA).