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.



ACATTAACATAACCAATATATACACCCATGATCAATGAGAACTCACATAAAAAAATATTTCTAGCCCTACCAAGGCGGTATCAACTACACCAAGGCGGTATCAACTACTAAACCAAGGCGGTATCAACTACTAATTTGGTCTATGTACACCGAGTTATAGACCAAACCAAGGCGGTATCCATAGACCAAACCAAGGCGACATAGACCAAACCAAGGCGACATAGACCAAACCAAGGCGGACATAGACCAAACCAAGGCGGTTACATAGACCAAACCAAGTACATAGACCAAACCAAGGCTACATAGACCAAACCAAGGCGGTACATAGACCAAACCAAGGTACATAGACCAAACCAAGGCTGTACATAGACCAAACCAAGGGTGTACATAGACCAAACCAAGGTGTACATAGACCAAACCAAGGCGGGTGTACATAGACCAAACCAACGGTGTACATAGACCAAACCATCGGTGTACATAGACCAAACTCGGTGTACATAGACCAAACCTCGGTGTACATAGACCAAACCACTCGGTGTACATAGACCAAACACTCGGTGTACATAGACCAAAAACTCGGTGTACATAGACAACTCGGTGTACATAGACCAACTCGGTGTACATAGACCAAACTCGGTGTACATAGACCAAAACTCGGTGTACATAGACCAAAAACTCGGTGTACATAGACCAAACAAACTCGGTGTACATAGACAAACTCGGTGTACATAGACCAAACTCGGTGTACATAGACCAAAACTCGGTGTACATAGACCAAAAAACTCGGTGTACATAGACCAAACCAAACTCGGTGTACATAGACCAAACTCGGTGTACATAGACCACAAACTCGGTGTACATAGAACAAACTCGGTGTACATAGACACAAACTCGGTGTACATAGACCAACAAACTCGGTGTACATAGAAACAAACTCGGTGTACATAGACGAACAAACTCGGTGTACATAGACCTGAACAAACTCGGTGTACATTGAACAAACTCGGTGTACATATGAACAAACTCGGTGTACATAGTGAACAAACTCGGTGTACATAGACACTGAACAAACTCGGTGTACACTGAACAAACTCGGTGTACATAACTGAACAAACTCGGTGTACATAGAACTGAACAAACTCGGTGTACGAACTGAACAAACTCGGTGGAACTGAACAAACTCGGTGTAGAACTGAACAAACTCGGTGAGAACTGAACAAACTCGGTGTAAGAACTGAACAAACTCGGAAGAACTGAACAAACTCGGTAAGAACTGAACAAACTCGGTGAAGAACTGAACAAACTCGGTGTAAGAACTGAACAAACTCGGTGTAAAGAACTGAACAAACTCGGTGTACAAAGAACTGAACAAACTCGGTAAAGAACTGAACAAACTCGGTGAAAGAACTGAACAAACTCGGTGTAAAGAACTGAACAAACTCGGTGTAGAAAGAACTGAACAAACTCGGTGAAAGAACTGAACAAACTCGGTGTAGAAAGAACTGAACAAACTCGAGAAAGAACTGAACAAACTCGGTAGAAAGAACTGAACAAACTCGGTGAGAAAGAACTGAACAAACTCGGTGTTAGAAAGAACTGAACAAACTTAGAAAGAACTGAACAAACTCTATAGAAAGAACTGAACAAACTCGGTGTTATATAGAAAGAACTGAACATAGGATGGAGCTGAACAATAGGATGGAGCTGAACATACTCAGGATGGAGCTGAACATACTCGGTGGATGGAGCTGAACATACTCGGTGATGGAGCTGAACATACTCGGTGTAACATACTCGGTGTACATAAACATACTCGGTGTACATAAACTACTCGGTGTACATAAACCAAGCCCCGAGTATGTTCAGCTCCATTACACCGAGTATGTTCAGCTCATGTACACCGAGTATGTTCAGCTATGTACACCGAGTATGTTTATGTACACCGAGTATGTTCAAACCAAGCCAAGGCGGTAGAAAACCAAGCCAAGGCGGTAGAAATATTATGTACACCGAGTATGTTTATGTACACCGAGTATGTTTTATGTACACCGAGTATGTTCTTTATGTACACCGAGTATGTTGTTTATGTACACCGAGTATTTGGTTTATGTACACCGAGTTGGTTTATGTACACCGAGTACTTGGTTTATGTACACCGAGGCTTGGTTTATGTACACCGAGGGCTTGGTTTATGTACACCGGCTTGGTTTATGTACACCGGGCTTGGTTTATGTACACCGATGGCTTGGTTTATGTACATGGCTTGGTTTATGTACACTGGCTTGGTTTATGTACACCTGGCTTGGTTTATGTACACCGTTGGCTTGGTTTATGTACTTGGCTTGGTTTATGTACATTGGCTTGGTTTATGTACACTTGGCTTGGTTTATGTACACCTTGGCTTGGTTTATGTACACCGCTTGGCTTGGTTTATGTACCTTGGCTTGGTTTATGTACACCTTGGCTTGGTTTATGTACACCCCTTGGCTTGGTTTATGTACCCTTGGCTTGGTTTATGTACATCTTATTAGAATCTGAAATCTGAGGTTATCTGACCGTAATAGCTATAAAAACTGCAGAATCACGATAAACTGCAGAATCACGATTTAGCCATAAGTAGGATGGAGAAAAGGAAAGTAGGATGGAGAAAAGGGCATClick to see list of reads 17,349,448 - 17,349,657 17,349,541 - 17,349,750 17,349,559 - 17,349,768 17,349,898 - 17,350,107 17,349,891 - 17,349,682 17,349,571 - 17,349,362 17,349,570 - 17,349,361 17,349,569 - 17,349,360 17,349,568 - 17,349,359 17,349,567 - 17,349,358 17,349,566 - 17,349,357 17,349,564 - 17,349,355 17,349,560 - 17,349,351 17,349,559 - 17,349,350 17,349,558 - 17,349,349 17,349,554 - 17,349,345 17,349,484 - 17,349,275 17,349,483 - 17,349,274 17,349,481 - 17,349,272 17,349,480 - 17,349,271 17,349,479 - 17,349,270 17,349,477 - 17,349,268 17,349,474 - 17,349,265 17,349,472 - 17,349,263 17,349,471 - 17,349,262 17,349,470 - 17,349,261 17,349,469 - 17,349,260 17,349,468 - 17,349,259 17,349,467 - 17,349,258 17,349,466 - 17,349,257 17,349,465 - 17,349,256 17,349,464 - 17,349,255 17,349,463 - 17,349,254 17,349,462 - 17,349,253 17,349,461 - 17,349,252 17,349,460 - 17,349,251 17,349,459 - 17,349,250 17,349,458 - 17,349,249 17,348,507 - 17,348,298 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-MIR778 2 c miRNA 17,349,574 17,349,437 1 No splice variant annotated
    Predicted function: miRNA