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.



TTGTTCCACAGATCTTCCTCTTGAACCTTCACAAGAAAGTCCCTGTTCACAAGAAAGTCCCTGTTCTCACAAGAAAGTCCCTGTTCACAAGAAAGTCCCTGTTCAGAACAGGGACTTTCTTGTGAAAAGTTCAGTACATCGACGTCAGTACATCGACGAGACATCGACGAGACGTGGACTATCGACGAGACGTGGACTGATGCTGCATCTTTCTCGACGAGACGTGGACTGACGAGACGTGGACTGATGCTACGTGGACTGATGCTGCATGGACTGATGCTGCATCTTTCTTGCATCAGTCCACGTCTCGTCGATGTCTTGAAGCTGAGCTTGGAGACAGAGACATTTGGTTATGTAGAATTTCTCGAGTGCGTAGAACCAACTGTGGCTTGGGGAAAGAGATGAAAGAGATGTGTTGAACGAAACGAGCTTAAGGACTTGTTGATAAACTTTCTCGGTGTTGAATGAATGCGGTATGAAAACATTAGATGTCTTTGTCTCAATAAAATTTGTCTGCCTAGGTCCTTCTTTTCTTTTCAATGTTCCTTCTTTTCTTTTCAATGTTCCTTCTTTTCTTTTCAATGTAAGGTCAACTTGCCGGACACCATGGCTCTGTTTCCTTCTTTTCTTGACCTTGGCTCTGTTTCCTTGACCTTGGCTCTGTTTCCTGTTGACCTTGGCTCTGTTTCCAGTTGACCTTGGCTCTGTTTCAAGTTGACCTTGGCTCTGAAGTTGACCTTGGCTCTGTAAGTTGACCTTGGCTCTGTTCAAGTTGACCTTGGCTCTCAAGTTGACCTTGGCTCTGCAAGTTGACCTTGGCTCTGTCAAGTTGACCTTGGCTCTGTTCAAGTTGACCTTGGCTCTGTTTGCAAGTTGACCTTGGCTCGCAAGTTGACCTTGGCTCTGCAAGTTGACCTTGGCTCTGGCAAGTTGACCTTGGCTCTGTGCAAGTTGACCTTGGCTCTGTTGCAAGTTGACCTTGGCTCTGTTTGGCAAGTTGACCTTGGCTGGCAAGTTGACCTTGGCTCGGCAAGTTGACCTTGGCTCTGGCAAGTTGACCTTGGCTCTGGGCAAGTTGACCTTGGCTCTGTGGCAAGTTGACCTTGGCTCTGTTCGGCAAGTTGACCTTGGCCGGCAAGTTGACCTTGGCTCGGCAAGTTGACCTTGGCTCCGGCAAGTTGACCTTGGCTCTCGGCAAGTTGACCTTGGCTCTGCGGCAAGTTGACCTTGGCTCTGTCGGCAAGTTGACCTTGGCTCTGTTCCGGCAAGTTGACCTTGGCCGGCAAGTTGACCTTGGCCCGGCAAGTTGACCTTGGCTCCGGCAAGTTGACCTTGGCTCCCGGCAAGTTGACCTTGGCTCTCCGGCAAGTTGACCTTGGCTCTGCCGGCAAGTTGACCTTGGCTCTGTCCGGCAAGTTGACCTTGGCTCTGTTCCGGCAAGTTGACCTTGGCTCTGTTTTCCGGCAAGTTGACCTTGTCCGGCAAGTTGACCTTGGTCCGGCAAGTTGACCTTGGCTCCGGCAAGTTGACCTTGGCTTCCGGCAAGTTGACCTTGGCTCTCCGGCAAGTTGACCTTGGCTCTTCCGGCAAGTTGACCTTGGCTCTGTCCGGCAAGTTGACCTTGGCTCTGTTCCGGCAAGTTGACCTTGGCTCTGTTTCCGGCAAGTTGACCTTGGCTCTGTTTGTCCGGCAAGTTGACCTTGGCGTCCGGCAAGTTGACCTTGGCTGTCCGGCAAGTTGACCTTGGCTCGTCCGGCAAGTTGACCTTGGCTCTGTCCGGCAAGTTGACCTTGGCTCTGTGTCCGGCAAGTTGACCTTGGCTGTCCGGCAAGTTGACCTTGGCTCGTGTCCGGCAAGTTGACCTTGGCGTGTCCGGCAAGTTGACCTTGGCTGGTGTCCGGCAAGTTGACCTTGGGGTGTCCGGCAAGTTGACCTTGGCTTTGGTGTCCGGCAAGTTGACTTTTGGTGTCCGGCAAGTTGACCTTGCCGATGTTATCAACAAATCTTCAAGGATGACTTGCCGATGTTATCCCAAGGATGACTTGCCGAGCCAAGGATGACTTGCCGGCCAAGGATGACTTGCCGAGCCAAGGATGACTTGCCGATAGCCAAGGATGACTTGCCAGCCAAGGATGACTTGCCGAGCCAAGGATGACTTGCCGAAGCCAAGGATGACTTGCCGATGAGCCAAGGATGACTTGCGAGCCAAGGATGACTTGCCGAGCCAAGGATGACTTGCCGGAGCCAAGGATGACTTGCCGAGAGCCAAGGATGACTTGCCGATGTGAGCCAAGGATGACTTGTGAGCCAAGGATGACTTGCTGAGCCAAGGATGACTTGCCTGAGCCAAGGATGACTTGCCGTGAGCCAAGGATGACTTGCCGATGAGCCAAGGATGACTTGCCGATTGAGCCAAGGATGACTTGCCGATGTTGAGCCAAGGATGACTTTTGAGCCAAGGATGACTTGTTGAGCCAAGGATGACTTGCTTGAGCCAAGGATGACTTGCCTTGAGCCAAGGATGACTTGCCGTTGAGCCAAGGATGACTTGCCGAATTGAGCCAAGGATGACTTGATTGAGCCAAGGATGACTTGCATTGAGCCAAGGATGACTTGCCATTGAGCCAAGGATGACTTGCCGATTGAGCCAAGGATGACTTGCCGATGAGATTGAGCCAAGGATGACTGAGATTGAGCCAAGGATGACTTGAGATTGAGCCAAGGATGACTTGATGAGATTGAGCCAAGGATGAAATGAGATTGAGCCAAGGATGAGAATGAGATTGAGCCAAGGAGAATGAGATTGAGCCAAGGAAAGAATGAGATTGAGCCAAGGAAGAATGAGATTGAGCCAAGGATGAAAGAATGAGATTGAGCCAAGAAAGAATGAGATTGAGCCAAGGAAAGAATGAGATTGAGCCAAGGATAAAGAATGAGATTGAGCCAAGGATGTAAAGAATGAGATTGAGCCAAGATTAAAGAATGAGATTGAGCCAAATTAAAGAATGAGATTGAGCAAATTAAAGAATGAGATTGAGCCAAATTAAAGAATGAGATTGAGCCAAAAATTAAAGAATGAGATTGAGCCTGGAAAAATTAAAGAATGAGATTAATTGTATCATAGAGTCTTGCAAACCCTAACTCATGATGAAGGTAAGTAAAAAAAAAAAAAAAGTAAAAAAAAAAAAAAAAGTAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACTAAAAAAAAAAAAAAAACTAAAAAAAAAAAAAAAACTATGTTGTGAGACGATCGATCGATATGTTGTGAGACGATCGATCGATAGClick to see list of reads 20,038,516 - 20,038,725 20,039,106 - 20,039,315 20,039,591 - 20,039,382 20,039,588 - 20,039,379 20,039,587 - 20,039,378 20,039,586 - 20,039,377 20,039,584 - 20,039,375 20,039,583 - 20,039,374 20,039,582 - 20,039,373 20,039,578 - 20,039,369 20,039,577 - 20,039,368 20,039,576 - 20,039,367 20,039,575 - 20,039,366 20,039,574 - 20,039,365 20,039,530 - 20,039,321 20,039,524 - 20,039,315 20,039,523 - 20,039,314 20,039,522 - 20,039,313 20,039,521 - 20,039,312 20,039,520 - 20,039,311 20,039,519 - 20,039,310 20,039,518 - 20,039,309 20,039,516 - 20,039,307 20,039,515 - 20,039,306 20,039,514 - 20,039,305 20,039,507 - 20,039,298 20,039,498 - 20,039,289 20,039,151 - 20,038,942 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-MIR169d 1 c miRNA 20,039,616 20,039,463 1 No splice variant annotated
    Predicted function: miRNA