Using RNase sequence specificity to refine the identification of RNA-protein binding regions

BMC Genomics

Table 1 Top 1% 6-bp motifs and their RNase digestion frequencies

human transcriptome (entropy=0.96)		detected RNA fragments (entropy=0.42)		adjusted frequencies (entropy=0.56)
6-bp	frequency	6-bp	frequency	6-bp	frequency
AAAAAA	0.0035	AATAAA	0.262	TCTACA	0.333
TTTTTT	0.0035	TCTACA	0.054	AATAAA	0.085
AAAAAT	0.0016	TTGAAT	0.033	TTGAAT	0.044
ATTTTT	0.0016	AACAGA	0.021	CCTACA	0.036
AAAATA	0.0015	AACAAG	0.019	AACAGA	0.024
TATTTT	0.0013	CCTACA	0.019	AACAAG	0.023
TAAAAA	0.0013	TCTGAA	0.018	TCTGAA	0.016
TTTTTA	0.0013	TTCAGA	0.014	TTCAGA	0.016
AAATAA	0.0013	ATTCTT	0.013	CGTGAA	0.011

ISSN: 1471-2164