CR1-1_Amn

Basic information Differential Expression Stage analysis Survival analysis Correlation analysis

DF ID	DF0001336
TE superfamily	CR1
TE class	LINE
Species	Amniota
Length	813
Kimura value	30.90
Tau index	0.0000
Description	CR1 (Chicken Repeat 1) retrotransposon, CR1-1_Amn subfamily
Comment	-
Sequence	CGAGAAAGGACTTGGGGTNGTGGTGGATAAAACTCTAAAACCTTCGGCACAGTGCTTAACAGCAGTNAAAAAAGCAAACAAAATNCTGGGATGCATAAATAGAGGTATCGAATATAAGTCGGAGGAAATTATTCTAGCACTGTATAAGGGACTAGTGAGGCCACATTTGGAATACTGTGCGCAGTTCTGGTCACCTTATTATAAAAAGGATATTATAGAAATGGAGAAGGTACAGCGGAGGGCAACCAGAATGATACAGGGACTCGGGGATCTTAGTTATTCAGAAAGGTTAGAGAAACTAGGTCTGTATTCTTTGGAAAAGAGGAGATTAAGAGGGGACCTCACTGAGGTATACANAATTCTGAAGGGAATAGAGAGGATAGATGCTACAAGGCTATTTGAGCTAGTGTCAAATACAAGAACAAGGGGGCACGAACTNAAGCTAAGGAAGGGCCGGGCACTAAAGGAATTTAGGCGGAATTTCTTTACGCAGAGNATAGTTAATATATGGAACTCATTGCCACAGGANGTCGTGGAGGCNAGNANTATAACCGGGTTCAAAAGGGGACTGGATAAATTCATGGAGGATAGGTCCATTAGTGGCTATTAAACAGAACGGNTAAGGAATGNTGTCCCTAGCCTCTGNTTGTCGGAGGGTGGAGANGGATGGCAGGAGANAGATCACTTGATCATTACCTGTTAGGTTCACTCCCTCTGAAGCATCTGGTACTGGCCACTGTCGGNAGACAGGATACTGGGCTAGATGGACCNTTGGTCTGACCCAGTATGGCAGTTCTTATGTTCTTATGTTCT

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
CR1-1_Amn	ZNF708	228	236	-	16.48	GCTGTACCT
CR1-1_Amn	pha-4	71	80	+	14.61	AAAGCAAACA
CR1-1_Amn	ROX1	418	429	-	14.31	CCCCTTGTTCTT
CR1-1_Amn	Stat6	310	319	-	14.02	TTCCAAAGAA
CR1-1_Amn	PRDM1	2	8	-	13.28	CTTTCTC
CR1-1_Amn	Nkx2-1	683	689	+	13.15	CACTTGA
CR1-1_Amn	unc-86	91	98	-	13.03	TTATGCAT
CR1-1_Amn	ARF3	648	655	+	12.99	TGTCGGAG
CR1-1_Amn	FOXC2	71	81	+	12.97	AAAGCAAACAA
CR1-1_Amn	LYS14	476	482	+	12.96	CGGAATT

1 2 3 4 ... 12

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).