Table 1.

Complete annotation of secondary structure defects in the stem region of wild-type pri-mir-16-1, pri-mir-30a, and pri-mir-107

Helical Imperfection	Found in	Sequence in RNA	SHAPE Detection	Single-stranded by Ribonucleases
U bulge	pri-mir-16-1	34-C--G-35 80-GUC-78	yes	no
U bulge	pri-mir-30a	8-U--G-9 84-AUC-82	yes	no
U bulge	pri-mir-107	25-CUU-27 76-G--G-75	yes	no
A bulge	pri-mir-30a	9-GAG-11 82-C--C-81	no	no
C bulge	pri-mir-107	41-CCU-43 61-G--A-60	no (small hit)	no
2-nt bulge	pri-mir-30a	25-CCUC-28 67-GG-66	yes	yes
2-nt bulge	pri-mir-107	16-UG-17 89-ACAC-86	yes	no (small hit)
1-by-1 symmetric internal loop*	pri-mir-16-1	23-CCU-25 91-GAA-89	no	no
1-by-1 symmetric internal loop	pri-mir-16-1	36-UAA-38 77-AAU-75	yes	yes
1-by-1 symmetric internal loop	pri-mir-16-1	45-GCG-47 68-CUC-66	no	no
1-by-1 symmetric internal loop	pri-mir-16-1	47-GUU-49 66-CUA-64	no	no
1-by-1 symmetric internal loop*	pri-mir-30a	13-GAC-15 79-UCG-77	no	no
1-by-1 symmetric internal loop	pri-mir-107	29-UUU-31 84-ACA-82	no(only C hit)	no (only C hit)
2-by-2 symmetric internal loop	pri-mir-16-1	18-CAGU-21 96-GGAA-93	no	no for T1; yes for A
1-by-3 asymmetric internal loop*	pri-mir-107	21-U--C--A-23 82-ACUAC-78	yes	yes

Helical imperfections that surround the Drosha cleavage site are indicated by an asterisk.