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.



ATATTTTAAAGTCATTGAAAATTTTCAATGACTTTAAAATATAATTCATTGTTAATGAATTAAATTATTTAACAGAATAATTTAATTCATTAATAGTAAAAATATAGAAAATCATAAAAAATATAATCGAATGTTTGACATATAATCGAATGTTTGACAAATATAATCGAATGTTTGACAAATAATCGAATGTTTGACAAAAAAAAATCGAATGTTTGACAAAAAAAGTAACATTCGATTATATTTTTTATGATTTTTGTCAAACATTCGATTATAAACAATATCTCTATTTTGATTATTTTTCACAATCTTGTAAAGTTATGATTATAGAAAACTCTCTAGCAATAGAAAACTCTCTAGCAATAGTTAATAGTTTATCAACAATGATCTGATAATTCCAAGAGTATGAATATACTCTTGGAATTATCAGATTTACATAATATTAGAAGTCACTAAATCACAAACCAATAACATCATCATGTTATTGGTTTGTGATTTAGTTCAGAATAGTAAACGCCGTTGATGACGTATAAGAAAATTTTAGGGTTTATGCTGGTTTTAGGTGAAACTCTGTAAATTTTGAAGCTTAACAGATTCTGATGGAAACTCTGTGTGATTTGATTGATTCGGTAGAACAACAAACAGAATAATTGTGGTCAGATCTGATAGTTGGACGGACTCCGATTCAGTTGATACACAGTTGATACAAGACGGGAGCTTGATACAAGACGGGAGCTCATTGATACAAGACGGGAGCTCACGTATCAACTGAATCGGAGTCCCTTGTATCAACTGAATCGGAGTCCTTGTATCAACTGAATCGGAGTCCTCTTGTATCAACTGAATCGGTCTTGTATCAACTGAATCGGATCTTGTATCAACTGAATCGGAGTCTTGTATCAACTGAATCGGAGTCTCTTGTATCAACTGAATCGGAGTCCGTCTTGTATCAACTGAATCGTCTTGTATCAACTGAATCGCGTCTTGTATCAACTGAATCGGAGCCGTCTTGTATCAACTGAATCCGTCTTGTATCAACTGAATCCCGTCTTGTATCAACTGAATCGGACCCGTCTTGTATCAACTGCCCGTCTTGTATCAACTGACCCGTCTTGTATCAACTGAACCCGTCTTGTATCAACTGAATCCCGTCTTGTATCAACTGAATCTCCCGTCTTGTATCAACTTCCCGTCTTGTATCAACTGTCCCGTCTTGTATCAACTGATCCCGTCTTGTATCAACTGAATCCCGTCTTGTATCAACTGAATTCCCGTCTTGTATCAACTGAATCCTCCCGTCTTGTATCAACCTCCCGTCTTGTATCAACTCTCCCGTCTTGTATCAACTGCTCCCGTCTTGTATCAACTGACTCCCGTCTTGTATCAACTGAACTCCCGTCTTGTATCAACTGAATGCTCCCGTCTTGTATCAACTGAATACAAACCAACCATGACAAGACACGTGAGCTCCCGTCTTGTATCAATCATGGTTGGTTTGTGAGCTCATGGTTGGTTTGTGAGCTCTTGTCATGGTTGGTTTGTGAGCCTTGTCATGGTTGGTTTGTGAGCTTCTTGTCATGGTTGGTTTGTGAGCGTGTCTTGTCATGGTTGGTTTGTCGTGTCTTGTCATGGTTGGTTTGTCGTGTCTTGTCATGGTTGGTTTGTGAGCTGACACGTGTCTTGTCATGGTTGGTTTGTGAGCTCCCGACCTGCACCAAGCGAATCCGACCTGCACCAAGCGAACGGGAACTGATTGGCTGACACCGACACGTGTAGGTCGGGAACTGATTGGCTGAGCAGGTCGGGAACTGATTGGCGGTGCAGGTCGGGAACTGAGGTGCAGGTCGGGAACTGATTGGCGGTGCAGGTCGGGAACTGATTGGCTTTGGTGCAGGTCGGGAACTTGGTGCAGGTCGGGAACTCTTGGTGCAGGTCGGGAACTTGGTGCAGGTCGGGAACCTTGGTGCAGGTCGGGAACTGCTTGGTGCAGGTCGGGAGCTTGGTGCAGGTCGGGAAGCTTGGTGCAGGTCGGGAACGCTTGGTGCAGGTCGGGAACTCGCTTGGTGCAGGTCGGGCGCTTGGTGCAGGTCGGGACGCTTGGTGCAGGTCGGGAACGCTTGGTGCAGGTCGGGAACCGCTTGGTGCAGGTCGGGAACTTCGCTTGGTGCAGGTCGGTCGCTTGGTGCAGGTCGGGTCGCTTGGTGCAGGTCGGGATCGCTTGGTGCAGGTCGGGAATCGCTTGGTGCAGGTCGGGAACTCGCTTGGTGCAGGTCGGGAACTTCGCTTGGTGCAGGTCGGGAACTGTCGCTTGGTGCAGGTCGGGAACTGATTCGCTTGGTGCAGGTCGGGTTCGCTTGGTGCAGGTCGGGATTCGCTTGGTGCAGGTCGGGAATTCGCTTGGTGCAGGTCGGGAACTTCGCTTGGTGCAGGTCGGGAACTATTCGCTTGGTGCAGGTCGGGATTCGCTTGGTGCAGGTCGGGAATTCGCTTGGTGCAGGTCGGGAAATTCGCTTGGTGCAGGTCGGGAACATTCGCTTGGTGCAGGTCGGGAACTGATTCGCTTGGTGCAGGTCGGGATTCGCTTGGTGCAGGTCGGGGATTCGCTTGGTGCAGGTCGGGAAGATTCGCTTGGTGCAGGTCGGGAACTGGATTCGCTTGGTGCAGGGGATTCGCTTGGTGCAGGTCGGATTCGCTTGGTGCAGGTCGGGATTCGCTTGGTGCAGGTCGGGGGATTCGCTTGGTGCAGGTCGGGACGGATTCGCTTGGTGCAGGTCGGATTCGCTTGGTGCAGGTCCGGATTCGCTTGGTGCAGGTCGGGCGGATTCGCTTGGTGCAGGTCGGGACGGATTCGCTTGGTGCAGGTCGGGAATCGGATTCGCTTGGTGCAGTCGGATTCGCTTGGTGCAGGTCGGTCGGATTCGCTTGGTGCAGGTCGGGCTCGGATTCGCTTGGTGCAGGCTCGGATTCGCTTGGTGCAGGTCTCGGATTCGCTTGGTGCAGGTCCTCGGATTCGCTTGGTGCAGGTCGTCTCGGATTCGCTTGGTGCAGTCTCGGATTCGCTTGGTGCAGGTCTCGGATTCGCTTGGTGCAGGTTCTCGGATTCGCTTGGTGCAGGTCTCTCGGATTCGCTTGGTGCAGGTCGCGGTCTCGGATTCGCTTGGTGGCGGTCTCGGATTCGCTTGGTGCATGATTGTTAAAGTTACCGGCGGATGATTGTTAAAGTTACCGGCGCGATGATTGTTAAAGTTACCGGCGACAGAAAAAATATTTGCCGGATTTGGTAACTGTATCGATAGTTGAGAAAGACCTAAAGAGACACGCGTAGACAAATAATTAACAGAAGACTTTTCAAAGAGACAATAGAAACAGAAGACTTTTCAACACCTGTGACTGTCACGTGCAACCTGTGACTGTCACGTGCATGCCTGTGACTGTCACGTGCATGCGGACTGAACCGGGATTTGTAAGCCAAACCGGACTGAACCGGGATTTTAATTATTAATCTAGCCAAACCGGACTGAACCAAAAAATCGTCTCTAAGAATGTAATGCAAAAAATCGTCTCTAAAGCAAAAAATCGTCTCTAAGAATGTACAAACTCTGGTGGCGAGGGGAGTGClick to see list of reads 18,357,956 - 18,358,165 18,358,806 - 18,359,015 18,358,809 - 18,359,018 18,358,875 - 18,359,084 18,359,160 - 18,359,369 18,359,162 - 18,359,371 18,359,328 - 18,359,119 18,358,923 - 18,358,714 18,358,904 - 18,358,695 18,358,901 - 18,358,692 18,358,900 - 18,358,691 18,358,898 - 18,358,689 18,358,897 - 18,358,688 18,358,896 - 18,358,687 18,358,895 - 18,358,686 18,358,894 - 18,358,685 18,358,893 - 18,358,684 18,358,892 - 18,358,683 18,358,891 - 18,358,682 18,358,884 - 18,358,675 18,358,829 - 18,358,620 18,358,825 - 18,358,616 18,358,824 - 18,358,615 18,358,823 - 18,358,614 18,358,822 - 18,358,613 18,358,821 - 18,358,612 18,358,819 - 18,358,610 18,358,815 - 18,358,606 18,358,032 - 18,357,823 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
AT5G45307 5 c miRNA 18,358,893 18,358,805 1 No splice variant annotated
    Predicted function: MIR168/MIR168B; miRNA