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.



AAGCCTCAAAAGATAACGAAGAGTAACTCTTCGTTATCTTTTGAGGCTAAGTAACTCTTCGTTATCTTTTGAAATACTTAGGCAAGTAACTCTATTTGATAAGGATTGAGTTACTAAGGATTGAGTTACAATTCAAGGATTGAGTTACAATTCTCCTTAATTAAGGAAGGAGAATTGTAACTTCCGATACACCGTTTTACACGAGAGATACACCGTTTTACACGAGATAGTCGGAAATTAAGGAAGGAGAATTCGGAAATTAAGGAAGGAGAATTATCGGAAATTAAGGAAGGAGAATTGTATCGGAAATTAAGGAAGGAGAGTATCGGAAATTAAGGAAGGAGAATGTATCGGAAATTAAGGAAGGAGACCGTTTTACACGAGATAGAGCCACGGTGTATCGGAAATTAAGGAAGGGGTGTATCGGAAATTAAGGAAGGAACGGTGTATCGGAAATTAAGGAAGTACACGAGATAGAGCCACCGGCATACACGAGATAGAGCCACCGGCACACACGAGATAGAGCCACCGGCACACACGAGATAGAGCCACCGGCACAACACGAGATAGAGCCACCGGCACATCACGAGATAGAGCCACCGGCACACACGAGATAGAGCCACCGGCACATGTAAAACGGTGTATCGGAAATTAAACGAGATAGAGCCACCGGCACACGAGATAGAGCCACCGGCACAACGAGATAGAGCCACCGGCACATACGAGATAGAGCCACCGGCACATCCGAGATAGAGCCACCGGCACATCAGTGTAAAACGGTGTATCGGAAATTGAGATAGAGCCACCGGCACGAGATAGAGCCACCGGCACATGAGATAGAGCCACCGGCACATCAGAGATAGAGCCACCGGCACATCACGATAGAGCCACCGGCACATCACCGATAGAGCCACCGGCACATCACATCTCGTGTAAAACGGTGTATCGTAGAGCCACCGGCACATCACCGAAGAGCCACCGGCACATCACCGATTGAGCCACCGGCACATCACCGAGAGCCACCGGCACATCACCGATTGAGCCACCGGCACATCACCGATTCAGCCACCGGCACATCACCGATTCATCTATCTCGTGTAAAACGGTTCTATCTCGTGTAAAACGGTGTAGCCACCGGCACATCACCGATTCGCCACCGGCACATCACCGATTCATCCACCGGCACATCACCGATTCCCACCGGCACATCACCGATTCACACCGGCACATCACCGATTCACCGGCACATCACCGATTCATCACCGGCACATCACCGATTCATAAACCGGCACATCACCGATTCATAACCGGCACATCACCGATTCATAACACCGGCACATCACCGATTCATAACTGGCACATCACCGATTCATAACTTGCCGGTGGCTCTATCTCGTGTATGCCGGTGGCTCTATCTCGTGTAATGTGCCGGTGGCTCTATCTCGTGTGTGCCGGTGGCTCTATCTCGTGTATGTGCCGGTGGCTCTATCTCGTGTCACCGATTCATAACTTTCACTCAGATGTGCCGGTGGCTCTATGATGTGCCGGTGGCTCTATCGATGTGCCGGTGGCTCTATCTCGTTGATGTGCCGGTGGCTCTATCTCGGGTGATGTGCCGGTGGCTCTGGTGATGTGCCGGTGGCTCTATCTGGTGATGTGCCGGTGGCTCTATCTCCGGTGATGTGCCGGTGGCTCCGGTGATGTGCCGGTGGCTCTATCTCGGTGATGTGCCGGTGGTCGGTGATGTGCCGGTGGCTCTCGGTGATGTGCCGGTGGCTCTAATCGGTGATGTGCCGGTGGCTATCGGTGATGTGCCGGTGGCTCATCGGTGATGTGCCGGTGGCTCTATCGGTGATGTGCCGGTGGCTCTAAATCGGTGATGTGCCGGTGGCAATCGGTGATGTGCCGGTGGCTAATCGGTGATGTGCCGGTGGCTCAATCGGTGATGTGCCGGTGGCTCTGAATCGGTGATGTGCCGGTGGAATCGGTGATGTGCCGGTGGGAATCGGTGATGTGCCGGTGGCGAATCGGTGATGTGCCGGTGGCTGAATCGGTGATGTGCCGGTGGCTCGAATCGGTGATGTGCCGGTGGCTCTATAACTTTCACTCACTCTAGCGATGAATCGGTGATGTGCCGGTGTGAATCGGTGATGTGCCGGTGGTGAATCGGTGATGTGCCGGTGGCTGAATCGGTGATGTGCCGGTGGCTTGAATCGGTGATGTGCCGGTGGCTCATGAATCGGTGATGTGCCATGAATCGGTGATGTGCCGGTGGATGAATCGGTGATGTGCCGGTGGCTATGAATCGGTGATGTGCCTATGAATCGGTGATGTGCCGGTGTATGAATCGGTGATGTGCCGGTGGTTATGAATCGGTGATGTGCCTTATGAATCGGTGATGTGCCGGTGGTTATGAATCGGTGATGTGCCGTTATGAATCGGTGATGTGCCGGTAGTTATGAATCGGTGATGTGCAGTTATGAATCGGTGATGTGCCAAGTTATGAATCGGTGATGTGCCAAAGTTATGAATCGGTGATGTGCCGTGAAAGTTATGAATCGGTGATGAGTGAAAGTTATGAATCGGTGATGTCTAGCGACACATACGTCACTGAACTAGCGACACATACGTCACTGCTAGCGACACATACGTCACTGAACGAGTGAGTGAAAGTTATGAATCGAGCGACACATACGTCACTGAACAAGCGACACATACGTCACTGAACAAACTGAACAAACATCAAACAATGCTGTTCAGTGACGTATGTGTCTTTATGCATTGTTTGATGCTTTATGCATTGTTTGATGTTCGATATGGAGGACGCTCACCGTATAAGTATACGTTCGGGCTAAACTCGGGACTGAAAGATAAAAGTAGACTTGAACCTGCTTAGTAGCGTGGTATGTGAACCTGCTTAGTAGCGGAAGAAACTCAAGAGGACCACTTAGTTGAGCAACTAGCATGAGATAGAGAGAGAGATATTACTTAAGAGAATTGTTGAGAGATCTGAAAACTAATTAAACTAAGGAGAAGATGAAGATCCTGAGGAGAAGATGAAGATCCTGGAGGAGAAGATGAAGATCCTGGTGAGAAGATGAAGATCCTGGTCAGAGAAGATGAAGATCCTGGTCATAGATGAAGATCCTGGTCATACTTGATGAAGATCCTGGTCATACTGGTCATACTTTTCCACAGCTGGTCATACTTTTCCACAGCTTCATACTTTTCCACAGCTTCATACTTTTCCACAGCTTTCATACTTTTCCACAGCTTTTCATACTTTTCCACAGCTTTCTCATACTTTTCCACAGCTTTCTTACTTTTCCACAGCTTTCTTTACTTTTCCACAGCTTTCTTGACTTTTCCACAGCTTTCTTGACTTTTCCACAGCTTTCTTGAATTTTCCACAGCTTTCTTGAACTTTTCCACAGCTTTCTTGAACTTTTTCCACAGCTTTCTTGAACTTTTTTCCACAGCTTTCTTGAACTTTTTTCCACAGCTTTCTTGAACTTTCCACAGCTTTCTTGAACTTTTCCACAGCTTTCTTGAACTTTTTCCACAGCTTTCTTGAACTTTTTCCACAGCTTTCTTGAATTCCACAGCTTTCTTGAACTTCCACAGCTTTCTTGAACTTTCCACAGCTTTCTTGAACTTTTCCACAGCTTTCTTGAACTTTTTCCACAGCTTTCTTGAACTTTCTTCCACAGCTTTCTTGAACTTTCTTTCCACAGCTTTCTTGAACTTTCTTTTCCACAGCTTTCTTGAACTTTCTTTTCCACAGCTTTCTTGAACTCCACAGCTTTCTTGAACTTCCACAGCTTTCTTGAACTTTCCACAGCTTTCTTGAACTTTCCACAGCTTTCTTGAACTCCACAGCTTTCTTGAACTTCCACAGCTTTCTTGAACTTTCACAGCTTTCTTGAACTTCACAGCTTTCTTGAACTTTCACAGCTTTCTTGAACTTTCCACAGCTTTCTTGAACTTTCTTACAGCTTTCTTGAACTTTACAGCTTTCTTGAACTTTCACAGCTTTCTTGAACTTTCTACAGCTTTCTTGAACTTTCTTTGTGGAAAAGTATGACCAGGAAGCTGTGGAAAAGTATGACCAGGAGCTGTGGAAAAGTATGACCAGGATTCAAGAAAGCTGTGGAAAAGGTTCAAGAAAGCTGTGGAAGTTCAAGAAAGCTGTGGAAAAAAGTTCAAGAAAGCTGTGGAAGAAAGTTCAAGAAAGCTGAGAAAGTTCAAGAAAGCTGTGGAAAACTTTAAGATTAAGCATTTTGGAAACTTTAAGATTAAGCATTTTGGAATTAAGCATTTTGGAAGCTCAAGAAAGCAGCATTTTGGAAGCTCAAGAAAGCATTTTGGAAGCTCAAGAAAGCTGTATTTTGGAAGCTCAAGAAAGCTTTTGGAAGCTCAAGAAAGCTTTTGGAAGCTCAAGAAAGCTGTTTGGAAGCTCAAGAAAGCTGTTTTGGAAGCTCAAGAAAGCTGTGGGAATTGGAAGCTCAAGAAAGCGAAGCTCAAGAAAGCTGTGGGAAGAAGCTCAAGAAAGCTGTGGGAAAAAGCTCAAGAAAGCTGTGAAGCTCAAGAAAGCTGTGGAAGCTCAAGAAAGCTGTGGGAAAGCTCAAGAAAGCTGTGGGAAAAGCTCAAGAAAGCTGTGGGAAAAGCTCAAGAAAGCTGTGGGAAAGCTCAAGAAAGCTGTGGGAAAGCTCAAGAAAGCTGTGGGGCTCAAGAAAGCTGTGGGAGCTCAAGAAAGCTGTGGGAAGCTCAAGAAAGCTGTGGGAAAGCTCAAGAAAGCTGTGGGAAAAGCTCAAGAAAGCTGTGGGAAAACCTCAAGAAAGCTGTGGGACTCAAGAAAGCTGTGGGAACTCAAGAAAGCTGTGGGAAACTCAAGAAAGCTGTGGGAAAACTCAAGAAAGCTGTGGGAAAACCTCAAGAAAGCTGTGGGAAAACATCAAGAAAGCTGTGGGAATCAAGAAAGCTGTGGGAAATCAAGAAAGCTGTGGGAAAATCAAGAAAGCTGTGGGAAAACCAAGAAAGCTGTGGGAAAAAGAAAGCTGTGGGAAAAAAGAAAGCTGTGGGAAAACATAAGAAAGCTGTGGGAAAACATGACAGAAAGCTGTGGGAAAACCTTGAGCTTCCAAAATGCTTAGAAAGCTGTGGGAAAACATGAAAGCTGTGGGAAAACATGACAAGCTGTGGGAAAACATGACAAGCTGTGGGAAAACATGACAAAGCTGTGGGAAAACATGACAAAAGCTGTGGGAAAACATGACAATAAGCTGTGGGAAAACATGACAATTAAGCTGTGGGAAAACATGACAATTCAAGCTGTGGGAAAACATGACAAGCTGTGGGAAAACATGACAAAGCTGTGGGAAAACATGACAATAGCTGTGGGAAAACATGACAATTTTCACTTGTCAAGATTCTTCTAGTGAATCAATGGAGTAAAACCCAGAAGAATCTTGACAAGTGAAAGAAGAATCTTGACAAGTGAAGATATTGATTTGAAGGTATTTTGGAAAGAAGAATCTTGACTTTGGAAAGAAGAATCTTGACAGATATTGATTTGAAGGTATATCAATATCTTTGGAAAGAAGAATTTCAAATCAATATCTTTGGATTATTCCTAAATTGAAGACACAGGTAAATTGAAGACACAGGATAACTAAATTGAAGACACAGGATAACAAATTGAAGACACAGGATAACTCTTATTGAAGACACAGGATAACTCTTGAAGACACAGGATAACTCTAGACACAGGATAACTCTTTAGATCCAGGATAACTCTTTAGATCTTTAGATCCATAATTATGGTCCATAATTATGGTCAGAATTATGGAATGGATCTAAAGAGTTATCCTTAATTATGGTCAGAATTATGGATCAATTATGGTCAGAATTATGGATCTATGGATCTAAAGAGTTATCCATTATGGTCAGAATTATGGAATTATGGTCAGAATTATGGATATTATGGTCAGAATTATGGATCTTATGGTCAGAATTATGGATTATGGTCAGAATTATGGATTATGGTCAGAATTATGGATCATGGTCAGAATTATGGATATGGTCAGAATTATGGATCTCAGAATTATGGATCTAAACAGAATTATGGATCTAAAGAGTAGAATTATGGATCTAAAGATATGGATCTAAAGAGTTATTGTATCCATAATTCTGACCATAATATCCATAATTCTGACCATAATTTTTAGATCCATAATTCTGACCACTCTTTAGATCCATAATTCTGACCTAAAGTACCGAAGACATTAGAAGTACCGAAGACATTAGGATGGTACCGAAGACATTAGGATGTACCGAAGACATTAGGATGGTAACCGAAGACATTAGGATGGTATCTTCGGTACTTTAGTGATTTCCTAATGTCTTCGGTACTTTAATCCTAATGTCTTCGGTACTTATCCTAATGTCTTCGGTACTTTCATGCTATAGTTAAATCTATAGGTATGTTGAGTTTTGTCCGACAAAACTCAACATACCTACGACAAAACTCAACATACCTTTTATTTACTTTCGACGACAAAACACTTTTATTTACTTTCGACGTATGTAGCCTTCATTGATACTATGTAGCCTTCATTGATACGTTATCATATGTAGCCTTCATTTTGGTTAATTGTGATAGTTTCTTCAAGGTTTTGTTTTAGATGTTTTGAAGATTTAGTAAGAAACTAACGAAGTTTCTGTGAGTTTCTGTAGAACTGGAAAGTGGAAATCATGTAGAACTGGAAAGAAAAGATCAGCATATAAACAAAAGATCAGCATATAAACCTTTATGTGATGTCACTCTAACCATGTGATGTCACTCTAACCACTCCACCTCCACTCTAACCACTCCACCTCAGGCGTCCACCTCAGGCGCGATTTACTCATACCGCGATTTACTCATACGTTTTTAAATCGCGCCTGAGGTGGAGGGAGGCATGTAGATATATATATATGTGGTCTCTATGTCTTTATTCACATGGTTTATATGCATGTGTGATCCATATAATTGTACATATATATACATAGAGATTGTATGACATGCACAATAGAGATTGTATGACATGCAAGAGATTGTATGACATGCAGAGATTGTATGACATGCACATTAATTTAACTTGGAGTTGGACTTTTCATATCAAATCAACATACTGTTTTTCATATCAAATCAACATACTGTTTATATCAAATCAACATACTGTTTCTCGTAAGTGCTTGGTTAACTGATTAGGAAAACCAAGCACTATATACCGTACGTCTTCTATGCTTAAGCACCAGTCGATCATATTCTTACAAAAGGATTATGTGCACCAGTCGATCTATTTGAAACTCCTAATGGATGGACCAAAACTTAAATTGTTAAGAATAGATCGGTCGATACTClick to see list of reads 13,610,952 - 13,611,161 13,611,009 - 13,611,218 13,611,011 - 13,611,220 13,611,014 - 13,611,223 13,611,017 - 13,611,226 13,611,020 - 13,611,229 13,611,057 - 13,611,266 13,611,778 - 13,611,987 13,611,779 - 13,611,988 13,611,796 - 13,612,005 13,611,797 - 13,612,006 13,611,800 - 13,612,009 13,611,803 - 13,612,012 13,611,804 - 13,612,013 13,611,805 - 13,612,014 13,611,806 - 13,612,015 13,611,807 - 13,612,016 13,611,808 - 13,612,017 13,611,809 - 13,612,018 13,611,812 - 13,612,021 13,611,892 - 13,612,101 13,611,895 - 13,612,104 13,611,896 - 13,612,105 13,611,897 - 13,612,106 13,611,902 - 13,612,111 13,611,903 - 13,612,112 13,611,904 - 13,612,113 13,611,905 - 13,612,114 13,611,906 - 13,612,115 13,611,908 - 13,612,117 13,611,911 - 13,612,120 13,611,912 - 13,612,121 13,611,913 - 13,612,122 13,611,955 - 13,612,164 13,612,025 - 13,612,234 13,612,027 - 13,612,236 13,612,028 - 13,612,237 13,612,048 - 13,612,257 13,612,060 - 13,612,269 13,612,107 - 13,612,316 13,612,114 - 13,612,323 13,612,165 - 13,612,374 13,612,356 - 13,612,565 13,612,449 - 13,612,658 13,612,483 - 13,612,692 13,612,757 - 13,612,966 13,612,760 - 13,612,969 13,613,137 - 13,613,346 13,612,491 - 13,612,282 13,612,424 - 13,612,215 13,612,393 - 13,612,184 13,612,291 - 13,612,082 13,612,254 - 13,612,045 13,612,248 - 13,612,039 13,612,187 - 13,611,978 13,612,130 - 13,611,921 13,612,085 - 13,611,876 13,612,080 - 13,611,871 13,612,059 - 13,611,850 13,612,058 - 13,611,849 13,611,982 - 13,611,773 13,611,976 - 13,611,767 13,611,910 - 13,611,701 13,611,829 - 13,611,620 13,611,827 - 13,611,618 13,611,825 - 13,611,616 13,611,814 - 13,611,605 13,611,701 - 13,611,492 13,611,643 - 13,611,434 13,611,102 - 13,610,893 13,611,046 - 13,610,837 13,611,045 - 13,610,836 13,611,041 - 13,610,832 13,611,040 - 13,610,831 13,611,039 - 13,610,830 13,611,038 - 13,610,829 13,611,037 - 13,610,828 13,610,944 - 13,610,735 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
AT5G35407 5 w miRNA 13,611,798 13,611,932 1 No splice variant annotated
    Predicted function: MIR396B; miRNA