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.



AGTATGGAGGAAGTGGGATTATTGATTGATTAGTATGGAGGAAGATTGAGAACTCTTTAGCCTTTATTGAGAACTCTTTAGCCTTTGGCTTCTGAGAACTCTTTAGCCTTTGGAGGAACAGAAGCCAAAGGCTAGAGATCTTGATGCTACTTCTGATCTTGATGCTACTTCTGTCCCTAGAAGTAGCATCAAGATCTCTAAGGGACAGAAGTAGCATCAAAAGTGATTTTACGTCGACCAACTATGGAAAGGGACAGAAGTAGCATGCTGATTCATTTGCTGTCTGAATAGCAAGAGGATTCAGACAGCAAAAAGCAAGAGGATTCAGACAGCAGGAAAGCAAGAGGATTCAGAGAGGAAAGCAAGAGGATTCAGCTTTCTCTGCGGTTGAAATAGCTAGAAAGATCCTTATCGGTTTCTAGCTAGGTTCTCGATGAATAGGCTTCTCGATGAATAGGCTAGCCTCTCGATGAATAGGCTAGCCTATCAGCCAGTAGTCGCAGATGCAGCCAGTAGTCGCAGATGCAGCACCAGTAGTCGCAGATGCAGCACCAGTAGTCGCAGATGCAGCACGTAGTCGCAGATGCAGCACCAGTAGTCGCAGATGCAGCACCATTAGTCGCAGATGCAGCACCAAGTCGCAGATGCAGCACCATTAAGCGCAGATGCAGCACCATTAAGATTCAGATGCAGCACCATTAAGATCAGATGCAGCACCATTAAGATTAGATGCAGCACCATTAAGATTAGATGCAGCACCATTAAGATTCATGCAGCACCATTAAGATTCACTGCAGCACCATTAAGATTCTGCAGCACCATTAAGATTCACTGCAGCACCATTAAGATTCACAGCAGCACCATTAAGATTCGCAGCACCATTAAGATTCAGCAGCACCATTAAGATTCACGCAGCACCATTAAGATTCACAGCAGCACCATTAAGATTCACAACAGCACCATTAAGATTCACCAGCACCATTAAGATTCACACAGCACCATTAAGATTCACAAAGCACCATTAAGATTCACAGCACCATTAAGATTCACAAGCACCATTAAGATTCACAAGGCACCATTAAGATTCACATGGTGCTGCATCTGCGACTTGGTGCTGCATCTGCGACTACTAATGGTGCTGCATCTGCGACTAATGGTGCTGCATCTGCGACTACTTAATGGTGCTGCATCTGCGACTACTTAATGGTGCTGCATCTGCGACTCTTAATGGTGCTGCATCTGTCTTAATGGTGCTGCATCTGCTCTTAATGGTGCTGCATCTGCGACATCTTAATGGTGCTGCATAATCTTAATGGTGCTGCATGAATCTTAATGGTGCTGCATGAATCTTAATGGTGCTGCATCGAATCTTAATGGTGCTGCATCTGACAAGAGATGTGGTTCCCTTTGCTTGAATCTTAATGGTGCTGTGAATCTTAATGGTGCTGCTGAATCTTAATGGTGCTGCATGAATCTTAATGGTGCTGCATTGAATCTTAATGGTGCTGCATCTGAATCTTAATGGTGCTGCATCTGTGAATCTTAATGGTGCTGCAGTGAATCTTAATGGTGCTGCATTGTGAATCTTAATGGTGCTGCTGTGAATCTTAATGGTGCTGCATTGTGAATCTTAATGGTGCTGCATCTTGTGAATCTTAATGGTGCTGCACTTGTGAATCTTAATGGTGCCTTGTGAATCTTAATGGTGCTGCTTGTGAATCTTAATGGTGCTGCCTTGTGAATCTTAATGGTGCTGCATCTTGTGAATCTTAATGGTGCTGCTCTTGTGAATCTTAATGGTGCTGCACTTTCGCCTCTCGATCCGCAGAAAAGGGTAGGCGAAAGCAAAGGGAACCAGATCCGCAGAAAAGGGTTCCTAAAGGGTTCCTTATCGAGTGGAAGGGTTCCTTATCGAGTGGAACCCTTTTCTGCGGATCGAAAGGAACCCTTTTCTGCGGATCGAGTATCGAGTGGGAATCTTGATGAATCGAGTGGGAATCTTGATGAGAGTGGGAATCTTGATGATGGAGTGGGAATCTTGATGATGCTGGAGTGGGAATCTTGATGATGCTGCGAGTGGGAATCTTGATGATGCTGCAAGTGGGAATCTTGATGATGCTAGTGGGAATCTTGATGATGCTGCAGTGGGAATCTTGATGATGCTGCAGTGGGAATCTTGATGATGCTGGTGGGAATCTTGATGATGCTGCAGTGGGAATCTTGATGATGCTGCATTGGGAATCTTGATGATGCTGGGAATCTTGATGATGCTGTGGGAATCTTGATGATGCTGCTGGGAATCTTGATGATGCTGCATGGGAATCTTGATGATGCTGCATGGGAATCTTGATGATGCTGGGAATCTTGATGATGCTGGGGAATCTTGATGATGCTGCGGGAATCTTGATGATGCTGCAGGGAATCTTGATGATGCTGCATGGGAATCTTGATGATGCTGCATCGGAATCTTGATGATGCTGGGAATCTTGATGATGCTGCGGAATCTTGATGATGCTGCAGGAATCTTGATGATGCTGCATGGAATCTTGATGATGCTGCATCGGAATCTTGATGATGCTGCATCAGGAATCTTGATGATGCTGCGAATCTTGATGATGCTGCAGAATCTTGATGATGCTGCATGAATCTTGATGATGCTGCATCAATCTTGATGATGCTGCAAATCTTGATGATGCTGCATAATCTTGATGATGCTGCATCATCTTGATGATGCTGCATATCTTGATGATGCTGCATCAGATCTTGATGATGCTGCATCAGCTCTTGATGATGCTGCATCAGTCTTGATGATGCTGCATCAGCCTTGATGATGCTGCATCAGCCTTGATGATGCTGCATCAGCACAGCATCATCAAGATTCCCACAGCATCATCAAGATTCCCACCAGCATCATCAAGATTCCCACTCGCAGCATCATCAAGATTCCCGCAGCATCATCAAGATTCCCATGCAGCATCATCAAGATTCTGCAGCATCATCAAGATTCCCTGATGCAGCATCATCAAGATTAATACATGGCTACTCTTGTCACTTTGCTGATGCAGCATCATCAATTTGCTGATGCAGCATCATCAAGTACATGGCTACTCTTGTCACTTATTTGCTGATGCAGCATCATCAAGAAGTGACAAGAGTAGCCATGTATTGAAGAGAGTAATGATGTCTTGAAATAGTGAGAACTCAGAAGTGAGTGGGAACTCACATGGTCACATACATGGTCACATGTGAGAATGGTTGGTCACATGTGAGAATGGTCCATAAGTGTTTGTTGGTCCCACATGGATCATATGAATCTCATCAGGAGTTGGGACCATTAGTGTGTCATCGCTTATGTATCTAACTCATGTTCGGTATTTTATAGTAACGAATGGCCTTAAAAGCTTTGACCTTGAATTGAAGACGGAACTAAAATGTTTGAATTGAAGACGGAACTATGTGTGTTTGTTTGATGTTTGATACATTCATGTAGTACATCTATACATGTAGTACATCTATATAAGAGAATATAAGAGAGAGTTTGGATCAAAATATAAGAGAGAGTTTGGATCAAAATAAGAGAGAGTTTGGATCAAGAGAGAGTTTGGATCAAAAAGAGAGAGTTTGGATCAAAAGAACTTAATCAAAAGAACTTAAAACATCCACTCTTGACTTTTGATCCAAACTCTCTCTCACTCTTGATTCATGGATGATTGGATGATGAAAATTTGTGGAClick to see list of reads 23,988,072 - 23,988,281 23,988,430 - 23,988,639 23,988,431 - 23,988,640 23,988,469 - 23,988,678 23,988,470 - 23,988,679 23,988,472 - 23,988,681 23,988,479 - 23,988,688 23,988,480 - 23,988,689 23,988,483 - 23,988,692 23,988,484 - 23,988,693 23,988,485 - 23,988,694 23,988,486 - 23,988,695 23,988,536 - 23,988,745 23,988,546 - 23,988,755 23,988,558 - 23,988,767 23,988,562 - 23,988,771 23,988,563 - 23,988,772 23,988,564 - 23,988,773 23,988,565 - 23,988,774 23,988,566 - 23,988,775 23,988,567 - 23,988,776 23,988,569 - 23,988,778 23,988,570 - 23,988,779 23,988,571 - 23,988,780 23,988,594 - 23,988,803 23,988,944 - 23,989,153 23,988,956 - 23,989,165 23,990,042 - 23,990,251 23,990,077 - 23,990,286 23,990,090 - 23,990,299 23,990,063 - 23,989,854 23,989,998 - 23,989,789 23,988,593 - 23,988,384 23,988,588 - 23,988,379 23,988,585 - 23,988,376 23,988,584 - 23,988,375 23,988,583 - 23,988,374 23,988,554 - 23,988,345 23,988,532 - 23,988,323 23,988,504 - 23,988,295 23,988,503 - 23,988,294 23,988,502 - 23,988,293 23,988,501 - 23,988,292 23,988,498 - 23,988,289 23,988,494 - 23,988,285 23,988,335 - 23,988,126 23,988,334 - 23,988,125 23,988,205 - 23,987,996 23,988,201 - 23,987,992 23,988,194 - 23,987,985 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
ath-MIR172e 5 w miRNA 23,988,472 23,988,596 1 No splice variant annotated
    Predicted function: miRNA