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.



TTAATACTTGTAGTCGCTAGGCTTAAGGGACATTATTAATTTTGAACTACAGAGATACATGCCTGATGCCTTTTCAGATAGTTTGAAGCTCATCAGGTCTCTTAGGGAATGGTTTAATCAGGTCTCTTAGGGAATGGTTATCAAAGAGATGACGACTCAGTATGAACATACCCACTGCGATATGAGAGATTTTTCGGTGATAAACAGTAAGTTTGAGAGATTTTTCGGTAAACCATTGGTCTTAGGGTAATCAACCTGAATCAAAGCACTGGACAGAAGCATATGGTAACTCAACCAGAAGCATATGGTAACTCAACATGCTTGACTCCTTGTACGCCGCTTGACTCCTTGTACGCCACCAAGGAGTCAAGCATGACCAGACAAGGAGTCAAGCATGACCTACAAGGAGTCAAGCATGATACAAGGAGTCAAGCATGACTACAAGGAGTCAAGCATGACCTACAAGGAGTCAAGCATGACCAGAGTACAAGGAGTCAAGCATGGTACAAGGAGTCAAGCATGACGTACAAGGAGTCAAGCACGTACAAGGAGTCAAGCATCGTACAAGGAGTCAAGCATGCGTACAAGGAGTCAAGCATGACGTACAAGGAGTCAAGCATGACGCGTACAAGGAGTCAAGCGCGTACAAGGAGTCAAGCAGCGTACAAGGAGTCAAGCATGCGTACAAGGAGTCAAGCATGGCGTACAAGGAGTCAAGCATGAGCGTACAAGGAGTCAAGCATGACGCGTACAAGGAGTCAAGCATGACCGGCGTACAAGGAGTCAAGGGCGTACAAGGAGTCAAGCATTGGCGTACAAGGAGTCAAGTGGCGTACAAGGAGTCAAGCAGTGGCGTACAAGGAGTCAGTGGCGTACAAGGAGTCAAGCGGTGGCGTACAAGGAGTCGGTGGCGTACAAGGAGTCAGGTGGCGTACAAGGAGTCAAGCGGTGGCGTACAAGGAGTCCCGGTGGCGTACAAGGAGTCCGGTGGCGTACAAGGAGTCGCCGGTGGCGTACAAGGAGTGCCGGTGGCGTACAAGGAGTCATGCCGGTGGCGTACAAGGAGTTGCCGGTGGCGTACAAGGAGTCCTGCCGGTGGCGTACAAGGAGTCTGCCGGTGGCGTACAAGGAGTCCTGCCGGTGGCGTACAAGGAGTCAGCTGCCGGTGGCGTACAAGGAGTCGCTGCCGGTGGCGTACAAGGAGTCAGGCTGCCGGTGGCGTACAAGGGGCTGCCGGTGGCGTACAAGGAGGCTGCCGGTGGCGTACAAGGAGTGGCTGCCGGTGGCGTACAAGGAGTCTCGGCTGCCGGTGGCGTACAAGGATCGGCTGCCGGTGGCGTACAAGGAGTCATCGGCTGCCGGTGGCGTATCGGCTGCCGGTGGCGTAATCGGCTGCCGGTGGCGTACATCGGCTGCCGGTGGCGTACAATCGGCTGCCGGTGGCGTACAAATCGGCTGCCGGTGGCGTACAAGATCGGCTGCCGGTGGCGTACAAGGATCGGCTGCCGGTGGCGTACAAGGAATCGGCTGCCGGTGGCGTACAAGGAGTAATCGGCTGCCGGTGGCGTACAAGGAGTAATCGGCTGCCGGTGGCGTACAAGGAGTCAAATCGGCTGCCGGTGGCGTACAAGGAGTCAAAATCGGCTGCCGGTGGCGTATAAAATCGGCTGCCGGTGGCGTACAAGGAGTTTAAAATCGGCTGCCGGTGTTTTAAAATCGGCTGCCGGTGGGTTTTAAAATCGGCTGCGGTTTTAAAATCGGCTGCCGGGGTTTTAAAATCGGCTGCCGGTGGGTTTTAAAATCGGCTGCCGGTGGTGGTTTTAAAATCGGCTGCCGTGGTTTTAAAATCGGCTGCCGGAAATCGGTATCCACTCGTGGCATATTGGTTTTAAAATCGGCTTTGGTTTTAAAATCGGCTGTTGGTTTTAAAATCGGCTGCCTTTGGTTTTAAAATCGGCTTTGGTTTTAAAATCGGCTTTTGGTTTTAAAATCGGCTGTTTGGTTTTAAAATCGGCTGCTTTGGTTTTAAAATCGGCTGCCTTTTGGTTTTAAAATCGGCTTTTTGGTTTTAAAATCGGCTGCTTTTGGTTTTAAAATCGGCTGCCATTTTGGTTTTAAAATCGGCTGATTTTGGTTTTAAAATCGGCTGCATACAGGGAGCCAGGCATTATGCCACGAGTGGATACCGATTTCTGTATGCCACGAGTGGATACCGATTTCCCTGTATGCCACGAGTGGATACCGATTCCCTGTATGCCACGAGTGGATACCGAGCTCCCTGTATGCCACGAGCTCCCTGTATGCCACGAGTGCTCCCTGTATGCCACGAGTGGATGCTCCCTGTATGCCACGAGTGGATAGCTCCCTGTATGCCACGAGTGGATACGCTCCCTGTATGCCACGAGTGGATACCGATTTGGCTCCCTGTATGCCACGAGCTGGCTCCCTGTATGCCACCTGGCTCCCTGTATGCCCCTGGCTCCCTGTATGCCACCTGGCTCCCTGTATGCCACGCCTGGCTCCCTGTATGCGCCTGGCTCCCTGTATGCCGCCTGGCTCCCTGTATGCCATGCCTGGCTCCCTGTATGTGCCTGGCTCCCTGTATGCTGCCTGGCTCCCTGTATGCCTGCCTGGCTCCCTGTATGCCATGCCTGGCTCCCTGTATGCCACTGCCTGGCTCCCTGTATGCCACGATGCCTGGCTCCCTGTATATGCCTGGCTCCCTGTATGATGCCTGGCTCCCTGTATGCATGCCTGGCTCCCTGTATGCCATGCCTGGCTCCCTGTATGCCATATGCCTGGCTCCCTGTATGCTATGCCTGGCTCCCTGTATGCCTATGCCTGGCTCCCTGTATGCCATTATGCCTGGCTCCCTGTATTATGCCTGGCTCCCTGTATTTATGCCTGGCTCCCTGTATGTTATGCCTGGCTCCCTGTATGCCATTTGTCGTTATGCCTGGCTTTGTCGTTATGCCTGGCTTTTGTCGTTATGCCTGGCTCTTTGTCGTTATGCCTGGCTCCTTTGTCGTTATGCCTGGCTCCCTTTTGTCGTTATGCCTGGCTCCCTGTTTGTCGTTATGCCTGGCTCCCTGTGTTTGTCGTTATGCCTGGCTCAGTTTGTCGTTATGCCTGGCTAGTTTGTCGTTATGCCTGGCAATAGTTTGTCGTTATGCCAATATATACATATAATAGTTTGTCGTTATGTGAACATATCTTTATACGTGGATCATGCGTAGAGGTTTGGTATATTCATGCGTAGAGGTTTGGTATGTTCATGCGTAGAGGTTTGGTTGTTCATGCGTAGAGGTTTGGTATAATCTTTATACGTGGATCTTGGATCTTTATACGTGGATCTTGGCTTATATGTTCATGCGTAGAGGTTTCTTTATACGTGGATCTTGGCTTTATACGTGGATCTTGGCTTTAAAGATATGTTCATGCGCTTTTTTTAACTGTTGGGAAGTTTTAACTGTTGGGAAGAGGAACAGTTAAAAAAAGTTCTGTGGGAAGAGGAAATGAAGTAGAAGAGGAAATGAAGTAGTCAGAGAGAGGAAATGAAGTAGTCAGAGTACTTCATTTCCTCTTCCCAACATCTGACTACTTCATTTCCTACTCTTCAACATTTCTCTCTGACTTGAAGAGGAATATGTGGTACAAAAGCATGACTAAGTTAGGTTTTGAACATTAAAGATTTTAAAAATCAAAAAATTGTTAACAAATTAAAGGACCAATTGTTAACAAATTAAAGGACCAACAAATTAAAGGACCCATTTACTAAAGGACCCATTTACTCACTTTCCAAGGAAAGTGAGTAAATGGGTCCTAATTCTTTGCATGATTTAACTCTCClick to see list of reads 19,008,899 - 19,009,108 19,009,099 - 19,009,308 19,009,237 - 19,009,446 19,009,238 - 19,009,447 19,009,240 - 19,009,449 19,009,275 - 19,009,484 19,009,279 - 19,009,488 19,009,289 - 19,009,498 19,009,295 - 19,009,504 19,009,238 - 19,009,029 19,009,233 - 19,009,024 19,009,191 - 19,008,982 19,009,189 - 19,008,980 19,009,188 - 19,008,979 19,009,181 - 19,008,972 19,009,180 - 19,008,971 19,009,179 - 19,008,970 19,009,178 - 19,008,969 19,009,174 - 19,008,965 19,009,144 - 19,008,935 19,009,142 - 19,008,933 19,009,141 - 19,008,932 19,009,140 - 19,008,931 19,009,139 - 19,008,930 19,009,130 - 19,008,921 19,009,127 - 19,008,918 19,009,124 - 19,008,915 19,009,120 - 19,008,911 19,009,119 - 19,008,910 19,009,118 - 19,008,909 19,009,117 - 19,008,908 19,009,116 - 19,008,907 19,009,115 - 19,008,906 19,009,113 - 19,008,904 19,009,111 - 19,008,902 19,009,093 - 19,008,884 19,008,631 - 19,008,422 19,008,209 - 19,008,000 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
AT5G46845 5 c miRNA 19,009,178 19,009,098 1 No splice variant annotated
    Predicted function: MIR160/MIR160C (MICRORNA160); miRNA