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.



AACGAATCATAAGTCTGAAAGAGAAAGAGAGAGAGAGAAGATTTTGAGGAAGAATTAATTTGTGCTTTGGTAGTAGATGAGGCTTTGGTAGTAGATGAGGTTTTTTGGTAGTAGATGAGGTTTAAAGAAATGGAAGGTATGGAGCATATATCAAAGGAAACATTGTATGCGGATATCAAAGGAAACATAAGTGCGGATATCAAAGGAAACATTAGAGAGTCCCTTTGATATAGAGAGTCCCTTTGATATTAGAGAGTCCCTTTGATATTGGAGAGAGTCCCTTTGATATTGGCAGAGAGTCCCTTTGATATTGGCCGAGAGTCCCTTTGATATTGGCCTGGAGAGTCCCTTTGATATTGGCAGAGTCCCTTTGATATTGGCCGAGTCCCTTTGATATTGGCCTGAGTCCCTTTGATATTGGCCTGAGTCCCTTTGATATTGGCCTGGGTCCCTTTGATATTGGCCTGGTTCCCTTTGATATTGGCCTGGTTCCCTTTGATATTGGCCTGGTTCCCTTTGATATTGGCCTGGTTCCCCTTTGATATTGGCCTGGTTCACCTTTGATATTGGCCTGGTTCCTTTGATATTGGCCTGGTTCCCTTTGATATTGGCCTGGTTCACCTTTGATATTGGCCTGGTTCACCCTTTGATATTGGCCTGGTTCACTCCTTTGATATTGGCCTGGTTCACTCCTTTGATATTGGCCTGGTTCCTTTGATATTGGCCTGGTTCATTTGATATTGGCCTGGTTCACTTGATATTGGCCTGGTTCACTCAGTGATATTGGCCTGGTTCACTCAGAGATATTGGCCTGGTTCACTCATATTGGCCTGGTTCACTCAGTATTGGCCTGGTTCACTCTATTGGCCTGGTTCACTCATATTGGCCTGGTTCACTCAGTATTGGCCTGGTTCACTCAGATATTGGCCTGGTTCACTCAGATTATTGGCCTGGTTCACTCAGATCTATTGGCCTGGTTCACTCAGATCTTATTGGCCTGGTTCACTCAGATCTTTATTGGCCTGGTTCACTCAGATCTTACCATTGGCCTGGTTCACTCAGAATTGGCCTGGTTCACTCAGATTTGGCCTGGTTCACTCAGATTGGCCTGGTTCACTCAGATCCACTCAGATCTTACCTGACCATAAGATCTGAGTGAACCAGGCTCTAGATTATCTGATTGAGCAGATTATCTGATTGAGCCGCGCTTATCTGATTGAGCCGCGCCAATATCTATCTGATTGAGCCGCGCCAATATCTGATTGAGCCGCGCCAATATCATCTGATTGAGCCGCGCCATCTGATTGAGCCGCGCCAAATCTGATTGAGCCGCGCCAATATCTGATTGAGCCGCGCCAATATCTCTGATTGAGCCGCGCCATCTGATTGAGCCGCGCCAATATCTGATTGAGCCGCGCCAATATCCTGATTGAGCCGCGCCAATACTGATTGAGCCGCGCCAATATCTGATTGAGCCGCGCCAATATCCTGATTGAGCCGCGCCAATATCTTGATTGAGCCGCGCCAATTGATTGAGCCGCGCCAATATGATTGAGCCGCGCCAATATTGATTGAGCCGCGCCAATATCTGATTGAGCCGCGCCAATATCTTGATTGAGCCGCGCCAATATCTCTGATTGAGCCGCGCCAATATCTCAGATTGAGCCGCGCCAATAGATTGAGCCGCGCCAATATCGATTGAGCCGCGCCAATATCTATTGAGCCGCGCCAATATATTGAGCCGCGCCAATATCATTGAGCCGCGCCAATATCTTTGAGCCGCGCCAATATCTGAGCCGCGCCAATATCTAGCCGCGCCAATATCTCAGAGCCGCGCCAATATCTCAGTAGCCGCGCCAATATCTCAGTAAGCCGCGCCAATATCTCAGTACAGCCGCGCCAATATCTCAGTACTGCCGCGCCAATATCTCAGTAGCCGCGCCAATATCTCAGTACCGCCAATATCTCAGTACTCTCGCCAATATCTCAGTACTCTCCGCCAATATCTCAGTACTCTCTCCAATATCTCAGTACTCTCTCAATATCTCAGTACTCTCCAATATCTCAGTACTCTCTCAATATCTCAGTACTCTCTCCAATATCTCAGTACTCTCTCGCAATATCTCAGTACTCTCTCGTAATATCTCAGTACTCTCTCGAATATCTCAGTACTCTCTCGTTGGCGCGGCTCAATCAGATAAATTGGCGCGGCTCAATCAGATAATAGATATTGGCGCGGCTCAATCAGTACTGAGATATTGGCGCGGCTCTCTCGTCTCTATTTTGGACGAGTACTGAGATATTGGCGCGAGAGTACTGAGATATTGGCGCAGAGTACTGAGATATTGGCGCGGCGAGAGTACTGAGATATTGGCGGAGAGAGTACTGAGATATTGGCGAGAGAGTACTGAGATATTGGCGCCAAAGTCCAAAATAGAGACGATTGTAGATCGATTTGTATGTGTTACAAATCGATCTACAAGACCTGTGTTGAAATGGAGACAAGTAAAGAAGTTACAAGTACTTGTCTCCTGAAAAATCAAGTCGTGTGTGATTTTTCAAGAATCTGGAAGTTATGGAGACACACACACGACTTAAGGCTTCCATGGAGACACACAAAAGGCTTCCATGGAGACACACAAGAAGAAATGGAAAAGGCTTTTGGAAAAGAAGAAATGGAAATTGGAAAAGAAGAAATGGAAAAAATGCATATTGTGTTGATACCATGTGTCAGCGAAACTGATCTTGTTTATTAGTACAATGCAGGATGTTAGAGAGTTCAGGATGTTAGAGAGTTAGTTAGCTAACTCTCTAACATCCTATTTTACATTGCTTCACCGGTTTTGCTTGTGATTGTGACATTTTACTTAATGAGAGAGAAGCTGACGAGCACAATGAGAGAGAAGCTGACGAGTGAGAGAGAAGCTGACGAGCAAGCTGACGAGCACGAACCCTAGCTGACGAGCACGAACCCTAACCTGCAGGTTAGGGTTCGTGCTCCTCACAAGCACTCCTCTAGCCACCGCCTCACAAGCACTCCTCTAGCCACCGCCTAGACTCTTCAATGCTTTAAACGCTAAAAAGGCTTGGATTTTAACGGCGGCAAAGGCTTGGATTTTAACGGCGTTTTAACGGCGGCAATCTCTTCTCGAGTGTTTCTGGAGCTGAAGAGCGATTTCTGGAGCTGAAGAGCGAACTGAAGAGCGAATGATTGTGCGAATGATTGTGATTCTGCTTGTGATTCTGCTTTGAGATATTCTGCTTTGAGATCGTCGGAGAAACAAACGTTTGGAGTTGGCCAAAACGTTTGGAGTTGGCCATGAAACGTTTGGAGTTGGCCATGTAAACGTTTGTTTGGTGTTGTAACCAAAAGAAGACAAGATCCATTGGTTTTAAAAGAGGACGTCTTAAAAGAGGACGTCTAAGGAGGACGTCTAAGGAAACGTAAGGGATATATGGAACATGATGTGCTGGGATATATGGAACATGATGTGCTCTCTATATGGAACATGATGTGCATGGAACATGATGTGCTCTCCTGGAACATGATGTGCTCTCCTCACTAACGAACGTGCTCGCATGTTAGTTAGAAATGAGGAGAGCTTAGTTAGAAATGAGGAGAGCAATTAGTAGTTTTCAAGACATTAGTAGTTTTCAAGACACACAGGGTGATTGTTGCATTTCAATGCGTAGATTTCACATGTGATTATAAAAATAAAATTAGGTCATTGGTATTGTTTGTAATATACTAATGACCCCCACTATGAATGTAATCGCGCTGAATGTAATCGCGCAGCCGGAAGAATGGTTCATCATClick to see list of reads 19,073,247 - 19,073,456 19,073,437 - 19,073,646 19,073,439 - 19,073,648 19,073,440 - 19,073,649 19,073,444 - 19,073,653 19,073,445 - 19,073,654 19,073,446 - 19,073,655 19,073,451 - 19,073,660 19,073,452 - 19,073,661 19,073,453 - 19,073,662 19,073,454 - 19,073,663 19,073,465 - 19,073,674 19,073,517 - 19,073,726 19,073,518 - 19,073,727 19,073,519 - 19,073,728 19,073,520 - 19,073,729 19,073,521 - 19,073,730 19,073,522 - 19,073,731 19,073,527 - 19,073,736 19,073,528 - 19,073,737 19,073,532 - 19,073,741 19,073,535 - 19,073,744 19,073,536 - 19,073,745 19,073,549 - 19,073,758 19,073,706 - 19,073,915 19,073,917 - 19,074,126 19,074,038 - 19,074,247 19,074,040 - 19,074,249 19,074,049 - 19,074,258 19,074,290 - 19,074,499 19,074,329 - 19,074,538 19,074,330 - 19,074,539 19,074,347 - 19,074,556 19,074,405 - 19,074,614 19,074,407 - 19,074,616 19,074,464 - 19,074,673 19,074,470 - 19,074,679 19,074,538 - 19,074,747 19,074,568 - 19,074,777 19,074,572 - 19,074,363 19,074,456 - 19,074,247 19,074,414 - 19,074,205 19,074,076 - 19,073,867 19,074,002 - 19,073,793 19,073,764 - 19,073,555 19,073,758 - 19,073,549 19,073,744 - 19,073,535 19,073,735 - 19,073,526 19,073,595 - 19,073,386 19,073,573 - 19,073,364 19,073,552 - 19,073,343 19,073,551 - 19,073,342 19,073,550 - 19,073,341 19,073,542 - 19,073,333 19,073,536 - 19,073,327 19,073,477 - 19,073,268 19,073,425 - 19,073,216 19,073,290 - 19,073,081 19,073,048 - 19,072,839 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-MIR171a 3 w miRNA 19,073,434 19,073,556 1 No splice variant annotated
    Predicted function: miRNA