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	NHLH2	716	731	-	7.29	AGTACCAGATGCTTCA
CR1-1_Amn	PLAG1	554	567	+	7.22	GGGTTCAAAAGGGG
CR1-1_Amn	TRP2	24	44	+	3.85	TGGATAAAACTCTAAAACCTT
CR1-1_Amn	RARA	228	244	+	3.74	AGGTACAGCGGAGGGCA
CR1-1_Amn	Rarb	553	568	+	-0.79	CGGGTTCAAAAGGGGA
CR1-1_Amn	ZAP1	691	705	-	-2.84	ACCTAACAGGTAATG
CR1-1_Amn	TRP1	25	45	+	-3.43	GGATAAAACTCTAAAACCTTC
CR1-1_Amn	RARA	554	571	+	-10.94	GGGTTCAAAAGGGGACTG

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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).