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.



TTTTAGGTGTAGAATTTACTAGAGGTTCCTTAAAGATGTCTGACTGAATTGTATTAATGTAAAGATGTCTGACAAACTGTAGCCCAATGTTATTTCATTACAAAAAACTGTAGCATTCATTACAAAAAACTGTAGATTCATTACAAAAAACTGTAGCATTCATTACAAAAAACTGTAGCCCTTCTCACGAATGTATATGAATTTCACGAATGTATATGAATTTTCATGTTTATCTTCTGCAGGCTCATAACATAAGTAAGAGCGTGATCCTAACATAAGTAAGAGCGTGATCCTAACATAAGTAAGAGCGTGATCCTATAAGTAAGAGCGTGATCCTCGACAAGTAAGAGCGTGATCCTCGACGAAGTAAGAGCGTGATCCTCGACGATAAGAGCGTGATCCTCGACGATTCCTCGACGATAGACATTGATAATTCGACGATAGACATTGATAATACCGTCGAGGATCACGCTCTTACTTATATCGTCGAGGATCACGCTCTTAGTCTATCGTCGAGGATCACGCTCAATGTCTATCGTCGAGGATCACGCCAATGTCTATCGTCGAGGAATCAATGTCTATCGTCGAGGATCATCAATGTCTATCGTCGAGGATCATATCAATGTCTATCGTCGAGGATTATCAATGTCTATCGTCGAGGATCTTATCAATGTCTATCGTCGAGGAATTATCAATGTCTATCGTCGAGGAAGGTATTATCAATGTCTATCGTCGAGAGATGAGGTATTATCAAAACTAACATAGAATCTTTAAACTCTATGTTAGTTGATGTGATCAATCAAGTCTATGTTAGTTGATGTGATCAATCAAGAGATTCTATGTTAGTTGATGTAAAGATTCTATGTTAGTTGATGTAAACTATTTAAACGCGTGATATTGACTATTTAAACGCGTGATATTGGCCTATTTAAACGCGTGATATTGTATTTAAACGCGTGATATTGGCACATTTAAACGCGTGATATTGGCACATTTAAACGCGTGATATTGGCACGAAACGCGTGATATTGGCACGGAAACGCGTGATATTGGCACGGCAAACGCGTGATATTGGCACGGCTCAACGCGTGATATTGGCACGGCTAACGCGTGATATTGGCACGGCTCAACGCGTGATATTGGCACGGCTCAACGCGTGATATTGGCACGGCTCAACGCGTGATATTGGCACGGCTCAACGCGTGATATTGGCACGGCTCACGCGTGATATTGGCACGGCTCAATGCGTGATATTGGCACGGCTCAATCCGTGATATTGGCACGGCTCAATCAGTGATATTGGCACGGCTCAATCAGTGATATTGGCACGGCTCAATCAATGATATTGGCACGGCTCAATGATATTGGCACGGCTCAATCTGATATTGGCACGGCTCAATCATGATATTGGCACGGCTCAATCAAGATATTGGCACGGCTCAATCGATATTGGCACGGCTCAATCAAGATATTGGCACGGCTCAATCAAATATATTGGCACGGCTCAATCATATTGGCACGGCTCAATCAATATTGGCACGGCTCAATCAAATCACGCGTTTAAATAGTTTAATCACGCGTTTAAATAGTTTAAAGTATTGGCACGGCTCAATCAAATATATCACGCGTTTAAATAGGGCACGGCTCAATCAAATAAACCCACGGCTCAATCAAATAAACACGGCTCAATCAAATAAACCGACGGCTCAATCAAATAAACCGTGCCAATATCACGCGTTTAAATAAGCCGTGCCAATATCACGGAGCCGTGCCAATATCACGAGCCGTGCCAATATCACGGAGCCGTGCCAATATCACGCGGAGCCGTGCCAATATCACGCGTTTGAGCCGTGCCAATATCACTGAGCCGTGCCAATATCACGTGAGCCGTGCCAATATCACGCGTTTTGAGCCGTGCCAATATCTTGAGCCGTGCCAATATCATTGAGCCGTGCCAATATCACTTGAGCCGTGCCAATATCACGTTGAGCCGTGCCAATATCACGCTTGAGCCGTGCCAATATCACGCGTTGAGCCGTGCCAATATCACGCGTATTGAGCCGTGCCAATATCAATTGAGCCGTGCCAATATCACGGATTGAGCCGTGCCAATATCTGATTGAGCCGTGCCAATTGATTGAGCCGTGCCAATATGATTGAGCCGTGCCAATATTGATTGAGCCGTGCCAATATCTGATTGAGCCGTGCCAATATCATGATTGAGCCGTGCCAATATCACTGATTGAGCCGTGCCAATATCACGTGATTGAGCCGTGCCAATATCACGCTTGATTGAGCCGTGCCAATATCACTTTGATTGAGCCGTGCCAATATCATTATTTGATTGAGCCGTGCCTTATTTGATTGAGCCGTGCCATTTATTTGATTGAGCCGTGCCGTTTATTTGATTGAGCCGGTTTATTTGATTGAGCCGTGCCAGGTTTATTTGATTGAGCCGTGCCAATCTTTAAAACAAAAGAGTACGGTTCGGTTTATTTGATTGAGCATCGGTTTATTTGATTGAGCCGTGTCTTTAAAACAAAAGAGTACGGATCGGTTTATTTGATTGAGGATCGGTTTATTTGATTGAGCCGTGAAAGATCGGTTTATTTGATTGAGCTTAAAGATCGGTTTATTTGATTGAACAAAAGAGTACGGTTTTCTGAACAAAAGAGTACGGTTTTCTGATTTTAAAGATCGGTTTATTTGATTTAAAGATCGGTTTATTTGATACAAAAGAGTACGGTTTTCTGATTTTTTAAAGATCGGTTTATTTGATTCAAAAGAGTACGGTTTTCTGAAAAAGAGTACGGTTTTCTGATTGATGTTTTAAAGATCGGTTTATTTGATGTTTTAAAGATCGGTTTATTTGATAAGAGTACGGTTTTCTGATTGAACTTTGTTTTAAAGATCGGTTTTGTTTTAAAGATCGGTTTATTTTTGTTTTAAAGATCGGTTTATTTTTTGTTTTAAAGATCGGTTTATTTGAAGAGTACGGTTTTCTGATTGAACAGAGTACGGTTTTCTGATTGAACCTTTTGTTTTAAAGATCGGTTTTGTTTTAAAGATCGGTTTTTGTTTTAAAGATCGGTTTATTCTTTTGTTTTAAAGATCGGTAGTACGGTTTTCTGATTGAACCTCTTTTGTTTTAAAGATCGGTTACGGTTTTCTGATTGAACCACGGTTTTCTGATTGAACCGCACCCGGTTTTCTGATTGAACCGCACCAGGTTTTCTGATTGAACCGCACGTTTTCTGATTGAACCGCACCATTTTCTGATTGAACCGCACCTGATTGAACCGCACCAATATCGATTGAACCGCACCAATATCTCGTTCAGAAAACCGTACTCTTTTGTTTTGAACCGCACCAATATCTTGAACCGCACCAATATCTCTTGAACCGCACCAATATCTCGTTGAACCGCACCAATATCTCGTTCAATCAGAAAACCGTACTCACCGCACCAATATCTCGTATTTGATTGGTGCGGTTCAATCAATTGGTGCGGTTCAATCAGATTGGTGCGGTTCAATCAGAAATTGGTGCGGTTCAATCAGAAAACTATTGGTGCGGTTCAATCTATTGGTGCGGTTCAATCAGTATTGGTGCGGTTCAATCAGAATATTGGTGCGGTTCAATCATATTGGTGCGGTTCAATCAGGATATTGGTGCGGTTCAAGATATTGGTGCGGTTCAATGATATTGGTGCGGTTCAATCGATATTGGTGCGGTTCAATCAGATATTGGTGCGGTTCAATCAGAAGATATTGGTGCGGTTCAAGATATTGGTGCGGTTCAAAGATATTGGTGCGGTTCAATAGATATTGGTGCGGTTCAATCAGATATTGGTGCGGTTCAATCAAGATATTGGTGCGGTTCAATCAGAGAGATATTGGTGCGGTTCAATGAGATATTGGTGCGGTTCAATCCGAGATATTGGTGCGGTTCACGAGATATTGGTGCGGTTCAAACGAGATATTGGTGCGGTTCACGAGATATTGGTGCGGTTCAACGAGATATTGGTGCGGTTCAAACGAGATATTGGTGCGGTTCAATACGAGATATTGGTGCGGTTCAATCACGAGATATTGGTGCGGTTCAATCATACGAGATATTGGTGCGGTACGAGATATTGGTGCGGTTACGAGATATTGGTGCGGTTTACGAGATATTGGTGCGGTTCTACGAGATATTGGTGCGGTTCATACGAGATATTGGTGCGGTTCAATACGAGATATTGGTGCGGTTCAATTACGAGATATTGGTGCGGTTCAATCAATACGAGATATTGGTGCGGTTCAATACGAGATATTGGTGCGGTTCAAAATACGAGATATTGGTGCGGTAATACGAGATATTGGTGCGGTTCAGATGTCCGATAGTGCGCTCAGATGTCCGATAGTGCGCTCATCTCGGACATCAAATACGAGATATTGGTGCCTATCGGACATCAAATACGAACTATCGGACATCAAATACGCACTATCGGACATCAAATACGAAGCGCACTATCGGACATCAAATACGAGCGCACTATCGGACATCAAATGATGAGCGCACTATCGGACATCGATGAGCGCACTATCGGACATCAGTCGATGAGCGCACTATCGGAAAGCAACTGAAGAGTCGATGAGATAAGCAACTGAAGAGTCGATATAAGCAACTGAAGAGTCGATGAGATGTGGATGGAGTTTGGTGTATATGTGGATGGAGTTTGGTGTATTTCTTTAATATGTGGATGGAGAAAGCAAGTAAATGATTGGAACAAATGATTGGAACAAATTGATAGGTATCCAATCATTTACTTGCTTTGGGTAAGTACCTGTCTCTAGTAACTTGTTTTCTAAACTGGTTTAACGTGCTAAAAAAAGAACCGTGTTAGAAAGAGACAACATGAGCTACTTGGGTTTGCAGAGTGAAAAAATATTTAGGTCGTCCGTTACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACAAAAAAAAAAAClick to see list of reads 22,929,958 - 22,930,167 22,930,084 - 22,930,293 22,930,090 - 22,930,299 22,930,097 - 22,930,306 22,930,099 - 22,930,308 22,930,129 - 22,930,338 22,930,138 - 22,930,347 22,930,149 - 22,930,358 22,930,156 - 22,930,365 22,930,159 - 22,930,368 22,930,393 - 22,930,602 22,930,380 - 22,930,171 22,930,303 - 22,930,094 22,930,245 - 22,930,036 22,930,224 - 22,930,015 22,930,209 - 22,930,000 22,930,183 - 22,929,974 22,930,181 - 22,929,972 22,930,180 - 22,929,971 22,930,179 - 22,929,970 22,930,178 - 22,929,969 22,930,177 - 22,929,968 22,930,176 - 22,929,967 22,930,175 - 22,929,966 22,930,174 - 22,929,965 22,930,173 - 22,929,964 22,930,144 - 22,929,935 22,930,136 - 22,929,927 22,930,124 - 22,929,915 22,930,123 - 22,929,914 22,930,118 - 22,929,909 22,930,115 - 22,929,906 22,930,113 - 22,929,904 22,930,100 - 22,929,891 22,930,078 - 22,929,869 22,929,745 - 22,929,536 22,929,744 - 22,929,535 22,929,657 - 22,929,448 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
AT1G62035 1 c miRNA 22,930,204 22,930,089 1 No splice variant annotated
    Predicted function: MIR171C; miRNA