Arabidopsis small RNA Gene Analysis

The basic information for the gene you have selected is displayed below. The "small RNA Information" section sums the reads that map to either strand of the gene of interest, indicating the total (normalized) read abundance, the count of distinct (different) sequences, and providing links to a downloadable file with that information, and web pages that provide detailed information on the complete set of individual sequences derived from the gene. View a legend that explains the icons and colors in the image below. Adjust libraries/reads or change display options on the control panel. In the control panel, you can show a special "phasing analysis" for small RNAs in this region.



GAGGACTCTGTTCCTAAAGCGATAGAATTTGGGTCGAAACTTGTCTGCGGAGAATTTGGGTCGAAACTTGAGGCTGGCCACTCTGAATCGCCTCTAAAACATCTGGTGTAGAATGTAACCTACACCAGATGTTTTACTGTAATGAGGACCTTTACAAAGACATAGAGAAATGTAAGCAGAACAAGGTAAGCAGAACAAGGTACACTAACTACAGAGAGAGCAAGAGAAACATGCACACTTGAACTGTTTTTAACCGGATTTTGTTGTAACGGCTAATTAAGATAAACCAAAAAGTCATAAAGGACTCTTCAAAGACGGATTTTGACTCTTCAAAGACGGATTTTGTTACTTCAAAGACGGATTTTGTCTTCAAAGACGGATTTTGTTCTTCAAAGACGGATTTTGTTATTCAAAGACGGATTTTGTTTTCAAAGACGGATTTTGTTATTCAAAGACGGATTTTGTTAATTCAAAGACGGATTTTGTTAACGTCAAAGACGGATTTTGTTAACAAAGACGGATTTTGTTAACGAAGACGGATTTTGTTAACGAAAGACGGATTTTGTTAACGAGACGGATTTTGTTAACGAAAACGGATTTTGTTAACGAAATCCGTCTTTGAAGAGTAAGCAAAATCCGTCTTTGAAGCAAAATCCGTCTTTGAAGAACAAAATCCGTCTTTGAAGACAAAATCCGTCTTTGAAGAAACAAAATCCGTCTTTGAAGAACAAAATCCGTCTTTGAAGATAACAAAATCCGTCTTTGATAACAAAATCCGTCTTTGAAGTTAACAAAATCCGTCTTTGTTAACAAAATCCGTCTTTGAATTAACAAAATCCGTCTTTGAAGTCGTTAACAAAATCCGTCTTTTCGTTAACAAAATCCGTCTTTTTCGTTAACAAAATCCGTCTTTCGTTAACAAAATCCGTCTTTTCGTTAACAAAATCCGTCTTTTAGTTAACAAAATCCGTTCCTAGTTAACAAAATCCGTTCCTTAGTTAACAAAATCCGTTCCTTACAAAATCCGTTCCTTGAAAAACAAAATCCGTTCCTTGAAAAGTTTTGTTAACTAAATGATTCATTTTGTTAACTAAATGATTATTTTGTTAACTAAATGATTCACGGATTTTGTTAACTAAAACGGATTTTGTTAACTAAATGACGGATTTTGTTAACTAAATGATTAACGGATTTTGTTAACTAAATAACGGATTTTGTTAACTAAATGAACGGATTTTGTTAACTAAATGATGAACGGATTTTGTTAACTGAACGGATTTTGTTAACTAAATAGGAACGGATTTTGTTAAAGGAACGGATTTTGTTAACTAGGAACGGATTTTGTTAACTAAGGAACGGATTTTGTTAACTAAAAGGAACGGATTTTGTTAAAGGAACGGATTTTGTTAAAAGGAACGGATTTTGTTAACAAGGAACGGATTTTGTTAACTAAAGGAACGGATTTTGTTAACTAAACAAGGAACGGATTTTGTTACAAGGAACGGATTTTGTTAACAAGGAACGGATTTTGTTAACCAAGGAACGGATTTTGTTAACTTCAAGGAACGGATTTTGTTCAAGGAACGGATTTTGTTTCAAGGAACGGATTTTGTTATCAAGGAACGGATTTTGTTAATCAAGGAACGGATTTTGTTAACTCAAGGAACGGATTTTGTTAACTTTCAAGGAACGGATTTTGTTCAAGGAACGGATTTTGTTTCAAGGAACGGATTTTGTTTTCAAGGAACGGATTTTGTTATTCAAGGAACGGATTTTGTTAATTCAAGGAACGGATTTTGTTAACTTCAAGGAACGGATTTTGTTAACTTTTCAAGGAACGGATTTTGTTTTTCAAGGAACGGATTTTGTTAACTTTTCAAGGAACGGATTTTGTACTTTTCAAGGAACGGATTTATAGATGATGATGATTGATGAAGGTCTAAGAGGGAGTAGTCTGTTClick to see list of reads 16,157,836 - 16,158,045 16,157,839 - 16,158,048 16,157,840 - 16,158,049 16,157,841 - 16,158,050 16,157,843 - 16,158,052 16,157,845 - 16,158,054 16,157,907 - 16,158,116 16,157,908 - 16,158,117 16,157,914 - 16,158,123 16,157,941 - 16,158,150 16,157,937 - 16,157,728 16,157,933 - 16,157,724 16,157,932 - 16,157,723 16,157,931 - 16,157,722 16,157,930 - 16,157,721 16,157,928 - 16,157,719 16,157,925 - 16,157,716 16,157,924 - 16,157,715 16,157,920 - 16,157,711 16,157,865 - 16,157,656 16,157,864 - 16,157,655 16,157,860 - 16,157,651 16,157,859 - 16,157,650 16,157,858 - 16,157,649 16,157,281 - 16,157,072 Click to see list of phasing windowsClick to see list of phasing windows
Gene map
Phasing analysis map
Phasing Analysis (above): Each dot represents a "window" of ten cycles of small RNAs of length 21 nt (where 21 is set in the control panel under Select phasing analysis options), with the score for the degree of phasing indicated on the Y axis (scores calculated approximately as described by Howell et al., 2007). The red dot is the highest scoring window and has the best score in this region. Other colored dots are windows which are in phase with the highest scoring window -- exactly-in-phase windows appear as filled dots, and almost-in-phase (-1/+1) windows as hollow dots. Only those reads corresponding to the featured length (the default length is 21 nt) are considered.

Gene Chr Strand Gene Type 5' End 3' End Model # of Splice Variants
AT5G40384 5 c miRNA 16,157,948 16,157,823 1 No splice variant annotated
    Predicted function: MIR866a; miRNA