Sulfolobus acidocaldarius sRNA Annotation

Name Ab Precip PE Conf Guide Box Target RNA Target Position Match/Mismatch Notes
sR1  D 16S U52 11/0 CDP,Mod 
sR2  D 23S C1914 11/0 CDP 
sR3  D 23S G2739 10/0 No Pause 
sR4  D 23S G1995 10/0  
sR5  F,N  D 16S G1056 12/0 CDP,Mod 
sR6  D 23S G2666 9/1  
sR7  D' 23S G2649 9/0 CDP 
      D 23S U2692 10/0 No Pause 
sR8  D' 23S U2972 9/1  
      D 23S G334 12/1  
sR9  D' 16S G926 8/0  
sR10  D' tRNA Gly-CCC C50 12/0  
      D 23S C2539 9/0  
sR11  D' 23S A2618 10/2  
sR12  D' 23S G1114  11/0  No Pause 
      D 23S A1134  10/1 CDP 
sR13  D' 23S G385 10/1  
      D 23S C2746 10/0 CDP 
sR14  F,N  D tRNA Gln-UUG U34 10/0  
sR15    ??       
sR16    ??       
sR17    ??      
sR18    F,N    D' 23S G140 9/1  
sR19      D 16S G672 9/1  
sR20      D' 23S C2065 11/0  
sR21        ??      
sR22      D' 23S C2916 11/0  
      D 23S U2893 10/0  
      D 16S U1310 10/1  
sR23        ??      
sR24        ??      
sR25        ??      
sR26        ??      
sR27        ??      
sR28      D 23S C473 10/0  
sR29        ??      

Ab Precip: the precipitations from which the respective sRNAs were recovered: F, antibody to aFIB; N, antibody to aNOP56. PE Conf: the presence of the sRNA in total cellular RNA was verified by primer extension. Guide Box: the position of the guide within the sRNA (D or D' box associated). Target RNA: predicted target of methylation. Target Position: predicted nucleotide postion of methylation. Match/Mismatch: the number of Watson-Crick and G-U matches / mismatches within the sRNA-target RNA duplex. Notes: "CDP", dNTP concentration-dependent primer extension pause observed at the predicted site of methylation, indicating a likely 2'-O-ribose methyl; "No Pause", no pause was detected at either high or low dNTP concentrations; "Mod", known site of nucleotide modification of unknown type in S. acidocaldarius 16S rRNA. Guides without notation were not experimentally examined.