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.



TTAGTGAAATCAAAAAGCTTATAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAAACCTAAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAACCTAAAAAAAAAAAAAAACCTTGTTCAAGCTGCAAATTCCACAGAACTTGTTCAAGCTGCAAATTCAACAGAACTTGTTCAAGCTAACAGAACTTGTTCAAGCTGCAAATTCCGTTATGGAAACAGAACTTGTTCAATGGAAACAGAACTTGTTCAAATGGAAACAGAACTTGTTCAAGCTGGATGGAAACAGAACTTGTAGGATGGAAACAGAACTTAGGATGGAAACAGAACTTGTAGGATGGAAACAGAACTTGTTGAGGATGGAAACAGAACTGAGGATGGAAACAGAACTTGTTCGAGGATGGAAACAGAACTTGTTCAATGAGGATGGAAACAGAACTGAGGATGGAAACAGAACTTTGAGGATGGAAACAGAATTGAGGATGGAAACAGAACTTTGAGGATGGAAACAGAACTTGTTTTGAGGATGGAAACAGAACTTTGAGGATGGAAACAGAACTTTTGAGGATGGAAACAGAACTTGTTTTGAGGATGGAAACAGAACTTGTTCAAGCTGCTTTTGAGGATGGAAACAGAACTTTTGAGGATGGAAACAGAACTTGTTTTTGAGGATGGAAACAGAACTTGTTCATTTTGAGGATGGAAACAGAACTTGTTCAAGCCTTTTGAGGATGGAAACAGAACTTGTCAAGAAAGGAAAATTTGGCTGGCTTTTGAGGATGGAAACAGAGCTTTTGAGGATGGAAACAGAACGCTTTTGAGGATGGAAACAGAACTTGCTTTTGAGGATGGAAACATTGCTTTTGAGGATGGAAACAGAAGCCAAATTTTCCTTTCTTGCTTTTGAGGATGTTACTTCAGCCAAATTTTCCTTTCTTAAGTTCTTGAAAGCACCTCTGTGAAGTTCTTGAAAGCACCCTCTGTGAAGTTCTTGAAACTCTGTGAAGTTCTTGAAAGCACCTTCTCTGTGAAGTTCTTGAAAGCTCTCTGTGAAGTTCTTGAAAGCTCTCTGTGAAGTTCTTGAAAGCACCTCCTGAGCTCTCTGTGAAGTTCTTGAAAGCACCTGGTTCAGAGCTCTCTGTGCATTACTGTTATGGTTCAGAGCTTTCATTACTGTTATGGTTCAGAGCTTTCATTACTGTTATGGTTCAGATTTCAGGTTTCATTACTGTTCTTCATGGCTTCTTCTGCTTGGGTCTGCTTAAAACTTCATGGCTATGGGTCTGCTTAAAACTAAATGGGTCTGCTTAAAACTTCATGGCTGAAATGGGTCTGCTTAAAACTTGAAATGGGTCTGCTTAAAACTTCATGGCTAGAAATGGGTCTGCTTAAAACTTCATTGAGAAATGGGTCTGCTTAAAACTGTTTGAGAAATGGGTCTGCTTAAAACTTCATGGCTGTTTGAGAAATGGGTCTGCTTAAAATTTGTTTGAGAAATGGGTCTGCATTTTGTTTGAGAAATGGGTCTGCTTAAAACCTGCATTTTGTTTGAGAAATAGAGTTTCATCTGCATTTTGTTAAGAGTTTCATCTGCATTTTGTTTGAGATTCTCTGTATGAATGATTGCATCATTATTCTCTGTATGAATGATTGCATCGCTTATAACTTTATTCTCTGTAGCCCATCGCTGTGATTTGCTCAGAATAATCCCAGTGTAGCCCAGAATAATCCCAGTGTAGCCCATCTAGAAGAAGACATTGTAGAGACTACAATGTCTTCTTCTACTTTGTCTCTTCACCAACACATTATCTCAGGGACATCAATACCAGAGTTTTCTTAATACTTGGGATGGTACCATTGTTTGAAAGAAATGGTACTATTCTTAATACTTAAGGACTTCTTTCAAACAATGGTTCAAGGACTTCTTTCAAACTCAAGGACTTCTTTCAAACATCAAGGACTTCTTTCAAACAATCAAGGACTTCTTTCAAACAATGTCAAGGACTTCTTTCAAACAATGGTGTCTTCAAGGACTTCTTATGTCTTCAAGGACTTCTTATATGTCTTCAAGGACTTCTATATGTCTTCAAGGACTTCTTATATGTCTTCAAGGACTTCTTTGATATGTCTTCAAGGACTGATATGTCTTCAAGGACTTGATATGTCTTCAAGGACTTCGATATGTCTTCAAGGACTTCTGATATGTCTTCAAGGACTTCTTGGATATGTCTTCAAGGACGGATATGTCTTCAAGGACTGGATATGTCTTCAAGGACTTGGATATGTCTTCAAGGACTTCGGATATGTCTTCAAGGACTTCTGGATATGTCTTCAAGGACTTCTTTGGATATGTCTTCAAGGACTTCTATGGATATGTCTTCAAGGACATGGATATGTCTTCAAGGACTATGGATATGTCTTCAAGGACTTATGGATATGTCTTCAAGGACTTCATGGATATGTCTTCAAGGACTTCTGATGGATATGTCTTCAAGGAGATGGATATGTCTTCAAGGACGATGGATATGTCTTCAAGGACTGATGGATATGTCTTCAAGGACTTGATGGATATGTCTTCAAGGACTTCTGATGGATATGTCTTCAAGGACTGATGGATATGTCTTCAAGGACTATGATGGATATGTCTTCAAGGACATGATGGATATGTCTTCAAGGACTCATGATGGATATGTCTTCAAGCATGATGGATATGTCTTCAAGGCATGATGGATATGTCTTCAAGGACATGATGGATATGTCTTCAAGGACCATGATGGATATGTCTTCAAGGACTTCATGATGGATATGTCTTCAAGGACAATGATTCTCATGATGGATATGTCAGAATGATTCTCATGATGGATACAAGAAGACGGACTCCATTGACATGGAGTCCGTCTTCTTGAGAAGCCATATTTCTCCAAGGACATCGAATATGCGTCAATGGAGTCCGTCTTGGAGAAATATGCGTCAATGGTTGGAGAAATATGCGTCAATTGGAGAAATATGCGTCAATTTGGAGAAATATGCGTCAATGGTTGGAGAAATATGCGTCAATGGACTTGGAGAAATATGCGTCAACCTTGGAGAAATATGCGTCCCTTGGAGAAATATGCGTCACCTTGGAGAAATATGCGTCAACCTTGGAGAAATATGCGTCAATCCTTGGAGAAATATGCGTCAATGCCTTGGAGAAATATGCGTCAATGGTCCTTGGAGAAATATGCGTTCCTTGGAGAAATATGCGTCATCCTTGGAGAAATATGCGTCAATCCTTGGAGAAATATGCGTCAATTGTCCTTGGAGAAATATGCGTTGTCCTTGGAGAAATATGCGTCAAATGTCCTTGGAGAAATATGCATGTCCTTGGAGAAATATGCGATGTCCTTGGAGAAATATGCGTATGTCCTTGGAGAAATATGCGTCATGTCCTTGGAGAAATATGCGTCAGATGTCCTTGGAGAAATATGCGATGTCCTTGGAGAAATATGCGGATGTCCTTGGAGAAATATGCGTGATGTCCTTGGAGAAATATGCGTCCGATGTCCTTGGAGAAATACGATGTCCTTGGAGAAATATGCGATGTCCTTGGAGAAATATGCCGATGTCCTTGGAGAAATATGCGCGATGTCCTTGGAGAAATATGCGTCGATGTCCTTGGAGAAATATGCGTCCGATGTCCTTGGAGAAATATGCGTCATTCGAACGATGTCCTTGGAGATTCGAACGATGTCCTTGGAGAAATTTCGAACGATGTCCTTGGAGTTTCGAACGATGTCCTTGGAGATTTCGAACGATGTCCTTGGAGAATTTCGAACGATGTCCTTGGAGAAATTTTCGAACGATGTCCTTGGATTTTCGAACGATGTCCTTGGAGTTTTCGAACGATGTCCTTGGAGATTTTCGAACGATGTCCTTGGAGAATTGTTTTCGAACGATGTCCTTGGAGATTGTTTTCGAACGATGTCCTTGATTGTTTTCGAACGATGTCCTTGGGGCTGATTTATGGAGTGTATAAATTGATTCAATCAAGCTCTGTCGATAATTTTGATAATGTTTAACGAATCTGAAAACAGAGAACTAGGACTTTCTGCTCTGATCACGTGTTTATATAAAGCTTACACTTCGTGAAGATTACATATCTGTGATTTGCATCTGTGATTTGCATTGTGAAATTCTGTAAGAACAACAAGCTGAAACACTClick to see list of reads 17,837,209 - 17,837,418 17,837,482 - 17,837,691 17,837,905 - 17,838,114 17,838,229 - 17,838,438 17,838,639 - 17,838,848 17,838,431 - 17,838,222 17,838,409 - 17,838,200 17,838,378 - 17,838,169 17,838,257 - 17,838,048 17,838,256 - 17,838,047 17,838,255 - 17,838,046 17,838,249 - 17,838,040 17,838,248 - 17,838,039 17,838,247 - 17,838,038 17,838,246 - 17,838,037 17,838,244 - 17,838,035 17,838,243 - 17,838,034 17,838,240 - 17,838,031 17,838,177 - 17,837,968 17,838,174 - 17,837,965 17,838,173 - 17,837,964 17,838,171 - 17,837,962 17,838,170 - 17,837,961 17,838,169 - 17,837,960 17,838,161 - 17,837,952 17,837,474 - 17,837,265 17,837,457 - 17,837,248 17,837,439 - 17,837,230 17,837,277 - 17,837,068 17,837,209 - 17,837,000 17,837,207 - 17,836,998 17,837,206 - 17,836,997 17,837,202 - 17,836,993 17,837,199 - 17,836,990 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
AT3G48201 3 c miRNA 17,838,266 17,838,135 1 No splice variant annotated
    Predicted function: MIR861a; miRNA