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.



GCATTTTAAAGTTAGGCTGATGAACGTAGTTAACCGGAACAGAATGTCAATGTGAGGTCTAGGAAATGCGAATTGGGTGAAGATCTTGTAGATTGGGTGAAGATCTTGTAGATTTGTGCAGTATGATCGTTATATATGCATTCAAATGCAGGGTGTAGATCATGCAAATGCAGGGTGTAGATCCAAATGCAGGGTGTAGATCATGTAAAATGCAGGGTGTAGATCATGTAATGCAGGGTGTAGATCATGTAGGTGTAGATCATGTAGTGATGAAATATAGTGTAGATCATGTAGTGATGATGTAGATCATGTAGTGATTGTAGATCATGTAGTGATGAAATATGTAGATCATGTAGTGATGAAATATATAGATCATGTAGTGATGAAATAGATCATGTAGTGATGAAATATACTGCTTCATGTAGTGATGAAATATACTGCTTCTGGGCTAATATACTGCTTCTGGGCATACTGCTTCTGGGCTCAAATACTGCTTCTGGGCTCAACAGATACTGCTTCTGGGCTCAACAGAGATAGCTGTTGCAAACTATGGTGCTGTTGCAAACTATGGTGATTACGGATTCTAACTAGTGGTTATATAACTAGTGGTTATAGCGATCGTTAGAATCCGTATAAGCTTCATATGATCGCTATAACCACTAACGGACTCAAAAGTATATATGATCTAAATGATGGACGGACTCAAACGGTTTTAAATGATGGACGGACCTGATAGTTGATCACGGTTTTATTGACAAACCAGCTTGCAGAATGAAGAAGCAAGCTGGTAGAATTTGCAAATGGGTTCACAGCGATTGCAAATGGGTTCACAGCGAAAATTCTTGAACCTGAAAACGCATTTGCAAATTCTTGAACCTGCATTTGCAAATTCTTGAACCTTCACAGCGATACGGGAGATGGGCAGCGATACGGGAGATGGGTTGCGATACGGGAGATGGGTTTTCCGACAAACGTACGGGAGATGGGTTTTCCGACGAGATGGGTTTTCCGACAAACGCTGCTCCCGTATCGCTGTGAACCCATTCGACAAACGCTGTTGCAGATGCTCACAGCGTTTGTCGGAAAACCCATCTGCAACAGCGTTTGTCGGCTTCATGTTTGAGAACGACCTTCATGTTTGAGAACGACACTGATAAGGAGAGAGCATCTGCAACAGCGTTTCATGTTTGAGAACGACACTGATAAGGCATTGATGTTTGAGAACGACACTGATAAGGCAATGTTTGAGAACGACACTGATAAGGCATTGGCAATGAAGAGAGCATCTGCAATGAAGAGAGCATCTGCAACAGTTTGAGAACGACACTGATAAGGCGTTTGAGAACGACACTGATAAGGCATTGGCAACATGAAGAGAGCATCTGCAATTTGAGAACGACACTGATAAGGCATTTGAGAACGACACTGATAAGGCATTGGCAAACATGAAGAGAGCATCTGCAAACATGAAGAGAGCATCTGCAATTGAGAACGACACTGATAAGGCATTTGAGAACGACACTGATAAGGCATTTTGAGAACGACACTGATAAGGCATTGGCATGAGAACGACACTGATAAGGCATGAGAACGACACTGATAAGGCATTGAGAACGACACTGATAAGGCATTTGAGAACGACACTGATAAGGCATTGGCACATTCAAACATGAAGAGAGCATCTGCGAGAACGACACTGATAAGGCAAGAACGACACTGATAAGGCATAGAACGACACTGATAAGGCATTGAGAACGACACTGATAAGGCATTGGCACAACGACACTGATAAGGCATTGGCACACGACACTGATAAGGCATTGGCACACGACACTGATAAGGCATTGGCACAACACTGATAAGGCATTGGCACATTTGCTTCAGTGTCGTTCTCAAACATGGTTCTTCCTAAATTTGGCTTTCCTAAATTTGGCTTTCAACTCTAAATTTGGCTTTCAACTCTAAATTTGGCTTTCAACTCTTTATCCTATAGTTTAGGAAGAACCATGGAGCAAAATTTGGCTTTCAACTCTTTATCATTTGGCTTTCAACTCTTTATCCTATTTGGCTTTCAACTCTTTATCCTATATTTGGCTTTCAACTCTTTATCCTATAGTTTTTTGGCTTTCAACTCTTTAACTCTTTATCCTATAGTTTATTAGGATAAAGAGTTGAAAGCTAGGATAAAGAGTTGAAAGCCACATAAAGATTGGTAAAGACATAAAGATTGGTAAAGTAAGATTGGTAAAGTATAGATTATTGGTAAAGTATAGATTATTGGGTTTATAGATTATTGGGTTTTACTATAGATTATTGGGTTTTACTTGCTTACTTGCTGTAAATGAATGATTTTTTGGAGTTTAACGTTTGTCAGTTTAACGTTTGTCGGTAAGAGTTTAACGTTTGTCGGTAAGAATATTTAACGTTTGTCGGTAAGATAACGTTTGTCGGTAAGACGTTTGTCGGTAAGAATATCTATTCCCACATCTCGGTAAGAATATCTATTCCCCGGTAAGAATATCTATTCCCGACAAACGTTAAACTCCAAAAAACCGACAAACGTTAAACTCTTACCGACAAACGTTAAACTCTGGGAATAGATATTCTTACCTTTGGATGTGGGAATAGATATTTTGGATGTGGGAATAGATATTCTTTCCTAGACTTCGTATAATGCATAGACTTCGTATAATGCAATGCCAATACGAAGTCTAGGATTTGGAATACGAAGTCTAGGATTTGGATATGGCAAGTTTAGAATACAATGTCATTTGTTCTTCTTTCCATTTGTCTGAAGAAAGCTATAAGCACCAAAGAGCCAAGATAGAGAAAGAAGAACAAATGACTATAGAGAAAGAAGAACAAATGACATTATAGAGAAAGAAGAACAAATGACATTTGCTTATAGAGAAAGAAGAACAAATGACATTTTCACACTTTGGATTCGTCTTTGGTCACTTTGGATTCGTCTTTGGTAAGTGTGAGGCTCTTGGCTAAGTGTGAGGCTCTTGGCTCTTCAAAGTGTGAGGCTCTTGGCTCCCAAAGTGTGAGGCTCTTGGCATTCGTCTTTGGTTCTACTAACGAATCCAAAGTGTGAGGCTGACGAATCCAAAGTGTGAGGCTCTCTACTACACTCCTGCGCATAAGTAGAACCAAAGACGAATCAGTAGAACCAAAGACGAATCCAAATAGTAGAACCAAAGACGAGTAGTAGAACCAAAGACGATGTAGTAGAACCAAAGACGAAAGTGTAGTAGAACCAAAGACGAATCCGAGTGTAGTAGAACCAAAGAGAGTGTAGTAGAACCAAAGACCGCAGGAGTGTAGTAGAACCTGCGCAGGAGTGTAGTAGAACGCCATATGCGCAGGAGTGTAGTAGAGCCATATGCGCAGGAGTGTAGTAGAAAGCCATATGCGCAGGAGTGTATTTACTTCCATACGTTTCAGAATAAGCAGTAGAAGCTAAGTCGCAGTAGAAGCTAAGTCATATATATACCTGAGGACCACGCATATACCTGAGGACCACGCAGAATATACCTGAGGACCACGCAGAACCCTGAGGACCACGCAGAACAGCTGAGGACCACGCAGAACAGCAAGAGGACCACGCAGAACAGCAAATTGCTGTTCTGCGTGGTCCTCAGGAAGGAAAGTTTTGCTGTTCTGTGAAGGAAAGTTTTGCTGTTCATGAAGGAAAGTTTTGCTGTTCATGTAGATGAAGGAAAGTTTAAGCATGTAGATGAAGGAAAGTTAAGCATGTAGATGAAGGAAATGTTAAGCATGTAGATGAAGGAATGTTAAGCATGTAGATGAAAAGACCCACAAACCATGAACCCTTGATGTTAAGCATGTAGACTTGATGTTAAGCATGTAGATGAAGGAAATGAACCCGTGCTGACGTCATCGTGCTGACGTCATCATGAGCAGCACGGGTTCATGGTTTGTGGGTCTTATGACGTCAGCACGGGTTCATAGCATACGAATGAAGAATGTCATGAAGAATGTCTCTGTCACCGGGGGTGACAGAGACATTCTTCATGGGGTGGGGGGGTGACAGGGGGGTGGGGGGGTGACAGGGGGTGGGGGGGTGACAGTGGGGGTGGGGGGGTGACTGGGGGTGGGGGGGTGACAGGTGGGGGTGGGGGGGTGAGTGGGGGTGGGGGGGTGACGTGGGGGTGGGGGGGTGACAGTGGGGGTGGGGGGGTGACAGGTGGGGGTGGGGGGGTGACAGATGGGGTGGGGGTGGGGGGGTGACAGAATGGGGTGGGGGTGGGGGGGTGACAGAAACTGAGTTTTTGTGTTGTCTGTTAACTGAGAGGTGAAACTGACACTGAGAGGTGAAACTGACCTTCAGTTACGCATGATGACACAGGCTAGATTTGTATCGATCAATAGTAACGCACGCATTGGCTAGGAGATGTATGTTATAACGCACGCATAATTCGGTGACAAGAAAGCGTGGAAATTCGGTGACAAGAATGGTGGAAATTCGGTGACAAGAAAGAACCAGAGTGGTGGAAATTCGGTGCAAATGGTATGAACCAGAGTGGACAAATGGTATGAACCAGAGTGGCAAGTTTTGATTTTCTGGCAGGAACCACCAAGTTTTGATTTTCTGGCAGATCAGACTGACAATATCCTGACAAATATAATCTTAACCAAGTTTTGATTTTCTGGCAGAGGCGAAGTCTTCTCAGAACCCAGGCGAAGTCTTCTCAGAACCATCAGGCGAAGTCTTCTCAGAACCAATCAGGCGAAGTCTTCTCAGAACAAATCAGGCGAAGTCTTCTCAGAACCACATCGGTTGCATGAAATCTCTGGAAAACCCACGGGCTTCTGGAAAACCCACGGGCTTACATCGGTCGCTTGCAGCACATCTGGAAAACCCATGCTCTGGGAACTACGCTTGCAGCACATTACGTAGATATTGTCGATGGCATATTGTCGATGGCTTTTGCATAACTGTTCTTTGCCTACGCTGCATGGACAAGAGCATTGATACTGAAAATACATGGACAAGAGCATTGATACTGAAAATAGTGCATGGACAAGAGCATTGATACAGCATGGACAAGAGCATTGATACTGAAGGGGACAGCATGGACAAGAAAGGGGACAGCATGGACAAGAGTTTTTGTGATATGTAGTGCAAATAGTGATTGCAAGATTTGTTATTGGAAGATGTGATTGCAAGATTTGTTATTTCGTCAAGCATGGATGGGGACTGCAGTTCGTCAAGCATGGATGGGGACTGTGCAGTTCGTCAAGCATGGATGGGGACTGAGGGATGCAGTTCGTCAAGCATGGATGGGGACTGGAGGGATGCAGTTCGTCAAGAAGAGGGATGCAGTTCGTCATCGGGATAATGACAAGTTTGGGTAGTGGTTATCGGGATAATGACAAGAAACCAAGAAAAGACCGTTAGTGACTTGCTGATGGAACTGAAAACTTGCTGATGGAACTGAAACCAAGAAAAGACCAACTTGCTGATGGAACTGAACAAACTTGCTGATGGAACTCCAAACTTGCTGATGGAACTGAAACCCCAAACTTGCTGATGGAACTGAAACCAAGAATGCCTAGCTGAACTTAATTCCAGCAGCTCTTGAGATGGAATCACTAGCAGCTCTTGAGAACACTAGCAGCTCTTGAGAACACTAGCAGCTCTTGAGATGGAGACACTAGCAGCTCTTGAGAGAAGACACTAGCAGCTCTTGAGAAGAAGACACTAGCAGCTCTAGAAGACACTAGCAGCTCTTGAGAAGAAGACACTAGCAGCTCTTGAGATAAGAAGACACTAGCAGCTCTTGAGAGAAGAAGACACTAGCAGCTCTTGGAAGAAGACACTAGCAGCTCTTGAGAAGAAGAAGACACTAGCAGCTCTTGAGAAGAAGACACTAGCAGCTCTTGAGATGGAATACAGAAGAAGACACTAGCAGCTCGAACAGAAGAAGACACTAGCAGCTCTTCATGGACTGTTGAAAACAGACTTTAATTTGTTTGGTCTTCTTTGAAGATCATAGCTTGCAGGTATCTGCTATATCAGTGGATGATATAACTTTCTGACATGACATTACTGATAGAGTAACCGGACAGGGCTCGATAGAGTAACCGGACAGTTCATCTAATCAATGAGCTCGATAGATGGCAAGAATCTCAAACTAGGATGGCAAGAATCTCAAACTTATGGCAAGAATCTCAAACTAGAAAATGTAGAGACGAGACCAATCTTCTATGTAGCAGGCCGCTTCTATGTAGCAGGCCGGTTCTTTTGCTCTTTATGTTTGCAAATATTCTCGAGCTCGATAATCAAGATTATCGAGCTCGAGAATAAGATTATCGAGCTCGAGAATATCAACCCATAAGATTATCGAGCTCGAGAATATCAACCAGTATAAGATTATCGAGCTTCGAGTATAAGATTATCGAGCTCAGAGATCTGATTTTGGATACTAAGAGATCTGATTTTGGAATTGCTTTGACTAAGAGATCTGATTGATTGCTTTGACTAAGAGATCTGGTCTGATTGCTTTGACTAAGACATTTGCGTCTGATTGCTTTGACTAAGAGATCTAGGCATTTGCGTCTGATTGCTTAGTGAAGAGGCATTTGCGTCTGATTGCTTTGACTTTCGACAGTGAAGAGGCATATTTGATCGAATTTCGACAAATTTGATCGAATTTCGACATTAGTGAAATTTGATCGATCTCCAGAAATCGGATTTTCTATCGGATTTTCTGGATCCAATGATTTCCGATTTCTGGAGATTTGAATTCTGGATCCAATGATTCGTCGCTGGATCCAATGATTCGTCGTGATCCAATGATTCGTCGTCACGATCCAATGATTCGTCGTCACTAGTGACGACGAATCATTGGATGAGTGACGACGAATCATTGGATTGAGTGACGACGAATCATTGGATCCATCGGTTTTATTTTGAGTGACGAATGTATCATTGGATCTGCAAAATGTATCATTGGATCTGCAACGGAGAATTGCAGATCCAATGCACAAACGGCGAGATCACTCACTTGATCTCGCCGTTTGTGTTCCGCTAAAAATTGGAATCTGGATTGAAAAATTGGAATCTGGATTGAAATTGGAATCTGGATTGAGAATCCAATTTTTCTCAGCGAAGTGATTCCAATTTTTCTCAGCGAAGTGAGTGTCTGGATTGAGAAATAAGGAGCTGGATTGAGAAATAAGGAGACTGGATTGAGAAATAAGGAGAGACTGGATTGAGAAATAAGGAGAGACATAAGGAGAGACAAGAGAAGAGAGAGTGCCGTTGAGATTTATGATGTCAATTTTGTGTGATCTTCTGATCAATTACCAAACCATAATCAAAAGAATCAGAGAGACTTTAACTCTACAATTTAATTCTGAGAATTAAATTGTAGAGTTTTCGAAACTGTCAAATATTACCGAAACTGTCAAATATTACCCTAGTAAAGAACACCTGATCCTTAAACGTCGTCGTCTTGACCTTTGACGAGAGTATTTGACGGCCCGATATTCTCTCTTCCATTTTTCCCCTTTTCGTGTGCTTCACAACTTCATCAAAAGGATGATGAAATGCAAAAAAAGGATGATGAAATGCAAAAATCGAAAAGGATGATGAAATGCATGAAGTTGTGAAGCACACGAATCTCGAGAGAATTTGCGTCATCTCGAGAGAGAGATGAAGTTGTCAATTCAAATCCTTTACGCAAATCCTTTACGCAAAGTTTCAAGGATTTGAATTGATGACGCAAAAGGATTTGAATTGATGACGCAAGGATTTGAATTGATGACGCAATTCAGTTTTTATTCACTTTCTTACATAACCTTATTCACTTTCTTACATAACCCTTATTCACTTTCTTACATAACCCATATAAAAACTGAAACTTTGCGTTTCTTACATAACCCATCAAACCAACTTACATAACCCATCAAACCAAATCCACATAACCCATCAAACCAAATCCTTAACCCATCAAACCAAATCCTACCCATCAAACCAAATCCTCGATCGGATCCATCAAACCAAATCCTCGATCGGATCATCAAACCAAATCCTCGCATCAAACCAAATCCTCGATCGGACATCAAACCAAATCCTCGATCGGATTATGTTATCAAACCAAATCCTCGATCGGAATCAAACCAAATCCTCGATCGGATATCAAACCAAATCCTCGATCGGATTATGTTTCAAACCAAATCCTCGATCGGATCAAACCAAATCCTCGATCGGATCAAACCAAATCCTCGATCGGACAAACCAAATCCTCGATCGGATAAACCAAATCCTCGATCGGAAAACCAAATCCTCGATCGGATAAACCAAATCCTCGATCGGATTATAACCAAATCCTCGATCGGAAACCAAATCCTCGATCGGATAACCAAATCCTCGATCGGATTAAACCAAATCCTCGATCGGATTATAACCAAATCCTCGATCGGATTATGTTAACCAAATCCTCGATCGGATTATGTTAAACCAAATCCTCGATCGGAACCAAATCCTCGATCGGATACCAAATCCTCGATCGGATTAACCAAATCCTCGATCGGATTATGCCAAATCCTCGATCGGATCCAAATCCTCGATCGGATTATCAAATCCTCGATCGGATTCAAATCCTCGATCGGATTATGTTTCCTCGATCGGATTATGTTAATCAATTCCTCGATCGGATTATGTTAATCCCTCGATCGGATTATGTTAATCAATTGCTCTCGATCGGATTATGTTAATCACTCGATCGGATTATGTTAATCAATTGCCTCGATCGGATTATGTTAATCAATTGCTCTCGATCGGATTATGTTAATCAATTGCTAAGATCGATCGGATTATGTTAATCAATCGATCGGATTATGTTAATCGATCGGATTATGTTAATCCGATCGGATTATGTTAATCAATTGCTAAGAGCGATCGGATTATGTTAATCGATCGGATTATGTTAATCAATCGGATTATGTTAATCAATATAATCCGATCGAGGATTTGGTAATCAATTGCTAAGAGCTTATTGCTAAGAGCTTTTTCTTCTCTTCTTCGCAATCCGCCATGGCClick to see list of reads 21,639,994 - 21,640,203 21,640,190 - 21,640,399 21,640,248 - 21,640,457 21,640,255 - 21,640,464 21,640,315 - 21,640,524 21,640,418 - 21,640,627 21,640,592 - 21,640,801 21,640,607 - 21,640,816 21,640,666 - 21,640,875 21,640,667 - 21,640,876 21,640,791 - 21,641,000 21,640,808 - 21,641,017 21,640,854 - 21,641,063 21,640,884 - 21,641,093 21,640,969 - 21,641,178 21,640,993 - 21,641,202 21,641,020 - 21,641,229 21,641,041 - 21,641,250 21,641,149 - 21,641,358 21,641,153 - 21,641,362 21,641,228 - 21,641,437 21,641,242 - 21,641,451 21,641,267 - 21,641,476 21,641,276 - 21,641,485 21,641,391 - 21,641,600 21,641,393 - 21,641,602 21,641,929 - 21,642,138 21,642,613 - 21,642,822 21,643,150 - 21,643,359 21,643,289 - 21,643,498 21,643,308 - 21,643,517 21,643,311 - 21,643,520 21,643,352 - 21,643,561 21,643,431 - 21,643,640 21,643,434 - 21,643,643 21,643,442 - 21,643,651 21,643,443 - 21,643,652 21,643,455 - 21,643,664 21,643,937 - 21,644,146 21,643,979 - 21,644,188 21,643,987 - 21,644,196 21,643,988 - 21,644,197 21,643,990 - 21,644,199 21,643,991 - 21,644,200 21,643,965 - 21,643,756 21,643,943 - 21,643,734 21,643,914 - 21,643,705 21,643,902 - 21,643,693 21,643,885 - 21,643,676 21,643,883 - 21,643,674 21,643,772 - 21,643,563 21,643,621 - 21,643,412 21,643,379 - 21,643,170 21,643,347 - 21,643,138 21,643,333 - 21,643,124 21,643,332 - 21,643,123 21,643,303 - 21,643,094 21,643,239 - 21,643,030 21,643,225 - 21,643,016 21,643,112 - 21,642,903 21,642,998 - 21,642,789 21,642,797 - 21,642,588 21,642,655 - 21,642,446 21,642,351 - 21,642,142 21,642,000 - 21,641,791 21,641,751 - 21,641,542 21,641,602 - 21,641,393 21,641,397 - 21,641,188 21,641,309 - 21,641,100 21,641,262 - 21,641,053 21,641,221 - 21,641,012 21,641,210 - 21,641,001 21,641,208 - 21,640,999 21,641,087 - 21,640,878 21,641,066 - 21,640,857 21,641,059 - 21,640,850 21,641,052 - 21,640,843 21,641,049 - 21,640,840 21,641,033 - 21,640,824 21,641,027 - 21,640,818 21,640,898 - 21,640,689 21,640,883 - 21,640,674 21,640,860 - 21,640,651 21,640,741 - 21,640,532 21,640,715 - 21,640,506 21,640,679 - 21,640,470 21,640,664 - 21,640,455 21,640,663 - 21,640,454 21,640,661 - 21,640,452 21,640,657 - 21,640,448 21,640,600 - 21,640,391 21,640,599 - 21,640,390 21,640,537 - 21,640,328 21,640,488 - 21,640,279 21,640,468 - 21,640,259 21,640,442 - 21,640,233 21,640,421 - 21,640,212 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
AT5G53340 5 c protein-coding 21,643,562 21,640,809 1 1
    Predicted function: Galactosyltransferase family protein