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.



AAAAAACAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAATAGTGTCGGAAAACAAACACAACACAAATAAAATTTACAGGATGACACAAATAAAATTTACAGGATACACAAATAAAATTTACAGGATGAATAAAATTTACAGGATGAAGAATTTACAGGATGAAGAATAGAAAAAGAGAAAAAGAAAAAAAAAAATTCTTTTTTTTTTTTCTTTTTAAAAGAGAGAGAGAAGTGGAGGAGAGAGAGAAGTGGAGAAGAGAGAGAGAAGTGGAGAAGAAGGAGAGAGAAGTGGAGAAGAAGAGAGAGAGAAGTGGAGAAGAAGATGAGAGAGAAGTGGAGAAGAAGAGAGAGAAGTGGAGAAGAAGATGGGGGAATCGAAGGAATAAGGTGAAAAATGGGGAATCGAAGGAATTATATTTTCTCCACCTCTCTGTCTTTTCTCCACCTCTCTGTCTTTTTCTCCACCTCTCTGTCTCCTATACACAGTTCTTCTCTGTTCCTCTAATCTATACACAGTTCTTCTCTGTAGGAAGCAAGCAAAAGAGACAAAGAACTGTGTATAGGAAGCAGAGAAGAACTGTGTATAGGAACGATTAGAGGAACAGAGAAGAAACAGAGGATCGAAGAATAAGACATTTCGTTCACCTCAATTGCAACCCAGATAGAAATTGACGAATTTTGTGTTAATCGAAGGAATTTTTGTGTTAATCGAAGGAATAAATCGAAGGAATAAGTGAATCAAGGAATAAGTGAATCGTCGTCTAAGGAATAAGTGAATCGTCGTCTTGGTAACTGATGCAGAAACCCTAAAATAACTGATGCAGAAACCCTATTGCTAGTTGTCGTTGAAGAAAGTTCAATAACTGATGCAGAAACCCTGTTGAAGAAAGCAGAAATTATAGTGTTGCTGATGGATTCTTGGAAATGAAACTCTTTTACCTTGTGATAAGATTTGAACAGAGACTCTCAGAGACTCTCTAATAATGATGTGTTGATTTCTGACATGTGTGTTGATTTCTGACATGGCTGTTGATTTCTGACATGGCTGATTTCTGACATGGCTGGTAACTCCAAGACATGGCTGGTAACTCCAAGACATGGCTGGTAACTCCAATGGAGTTGTTCCTGAAGAGGAAGATGAGGAAGATGAGGAGAACGAGGAAGATGAGGAGAACAAGGAAGATGAGGAGAACACTAGTCAGGAATTGAATAGGATTAGAGAACTTTGAAGAAGAAGAAGGAATTGAATAGGATAGATTGACTAGAGAACTTTGAAGAAGGAATTGAATAGGATAGATGGATAGATTTCAAACTTAGGACTTTTTGGATTTAGGAAATGATTTGCTCTGCCATCTAAATGTGTCAAGTTTATGGGTTCAAGTTTATGGGTGTAGTAAGGAAGTTTATGGGTGTAGTAAGGATTATGGGTGTAGTAAGGATCTGGGTGTAGTAAGGATCTGAGCTCTTTAGTAAGGATCTGAGCTCTTAAGGATCTGAGCTCTTCGAAAATCTGAGCTCTTCGAAAGAGGTTTTGTCAACAGTGCAGCAGCCTCTGTTCAAGACCATTAACTTGCACTGTTGACAAAACCTCTGTTCTGCACTGTTGACAAAACCTCTTCTTTTGCCATCATCAAACTGGTCACAATGAACGAAGAAGGAAACCTCACAATGAACGAAGAAGGAAACAATGAACGAAGAAGGAAACCAAGAAGGAAACCTGCATTCTAAGATGTAGTAGGCAACAAGTTTGTAGTAGGCAACAAGTTTCTGGAGAAAGTAGGCAACAAGTTTCTGAGTTTCTGGAGAATTCATCATTGGTTCTGGAGAATTCATCATTTACAGAGTAATAGATGAAGACGACAGTAATAGATGAAGACGACCACTAGATGAAGACGACCACCGTAGACGACCACCGTACAAGTAGACTCGTCACCGTACAAGTAGACTCGTGACCGTACAAGTAGACTCGTGAGACGGTGGTCGTCTTCATCTATGAAACATGGAACAAGTAGGTTTAATGAGCAAAACAGCAGCAGAACTTATGAATCAGCAAAACAGCAGCAGAACTTCAGCAGAACTTATGAATCGATTCATAAGTTCTGCTGCCACGGAAGTATCCTCCATTTGGGCATTTGGGACTTACATGAGACGGCGGCATCACGCGGGACTTACATGAGACGGCGGCAGACGGCGGCATCACGCTCTACGGCATCACGCTCTACTCGTGCTGCCGCCGTCTCATGTAAGTCAGAGCACGAGTAGAGCGTGATGCCGAGAGCACGAGTAGAGCGTGAGAGAGAGCACGAGTAGAGCGTAGAGAGAGCACGAGTAGAGCGTCTTCTGTCAGCTCAGTCCTCTTCTGTCAGCTCAGTCCCACAGAAGAGAGAGAGCACGACAGAAGAGAGAGAGCAGACAGAAGAGAGAGAGCACTGACAGAAGAGAGAGAGCTGACAGAAGAGAGAGAGCATGACAGAAGAGAGAGAGCACTGACAGAAGAGAGAGAGCACGCTGACAGAAGAGAGAGAGCACTGACAGAAGAGAGAGAGCACGGACTGAGCTGACAGAAGAGAGAGACAAGTGTTGTTGGGACTGGTTGTGGATCGATCCTGGCAAGACCAGGATCGATCCACAACGGTAAGAACTAGAACCAGCAGAATTGGAGGAAAAGGAACATCCACGGTTGATCTACTCACGGTTGATCTACTGCAACTACGGTTGATCTACTGCAACTGTTGCAGTAGATCAACCGTGGATGCAGGAATATAATGAGCTTTATTTTTGAGATTGTTCTGCAGAACTGCAGAAGGACAAGACAAGCCTGCAGAAGGACAAGACAAGCCTAGAAGGACAAGACAAGCCTAGGACAAGACAAGCCTGCATGCTGCATGGCTTGATTAGTTTGTGATTAGATTAAGAGGATCAGATCATGTTACACGTAGTTACACGTATTATTGTATTATTGTAATTTGTAACTGCACCAGTCAATAATGTTCTGAAAAGGAAGTAGGCATAGATATCTTAACGCTGTGAAAAGGAAGTAGGCATTCTGTAACGCTGTGAAAAGGAAATTTGTATATATACATGCAAATTGTCTGTAACGCTGTGAAGTTCTGTACACTCACGTCATCTGAGTCTGTACACTCACGTCATCTACACTCACGTCATCTGAGGACCTCACGTCATCTGAGGACTCTGAGGACTGATCTGAGATTCTCAGGACTGATCTGAGATTCTCGAGTTTTCGAACTCGAGAATCTCAGATCAACATCGTAACTTCGAACTTTTTGATAGGATTAAGACAAATAATTAAGACAAATAAAGACCATTTGAAAGTAACGTCACTTCTGTCTGTCTTTAGATTTGATTCTGTCTGTCTTTAGATTACGACGCAGCCACTCGCACTGCACGTGTGCGAGTGGCTGCGGAAGTGAACAAAACTCAGGGGAAAAGCGGTGAGAAGAAGTGAACAAAACTTCGGTGAGAAGAAGTGAACAAATCGGTGAGAAGAAGTGAACAAAACATTCGGTGAGAAGAAGTGAACAAAACTGGGATTCGGTGAGAAGAAGTGGGGATTCGGTGAGAAGAAGTGAACAAAACTCAGGGCTTGGGATTCGGTGAGAAGAGCCACAACATGATCCATGTTTCCGGATTGGCACTTTTGATGCTCCGGATTGGCACTTTTGATGCGTAAGCGGTTGTATGCAGATGGGAATTATCTGTTGAACATCTTTGGTATTTCACCTCCCTTTGTCGTCAAAGAGGAAGAGGAAGAAGAAGAAGGAAGAGGAAGAAGAAGACTTCTTCTTCCTCTTCCTAGTGACTATAAGAAGGGAAGCTAGTGACTATAAGAAGGGAAGCTCGGTGGAAGTGACTATAAGAAGGGAAGTGGTGGAAGTGACTATAAGAAGATGCAGAGCTTTGGTGGATGCGGCCATTGTGGTAACCTGAAATGCGGCCATTGTGGTAACCTCTCGTTTAAGAGAATGCTTGACACGGTAATTGAAGAGAATGCTTGACACGGTTGAAGAGAATGCTTGACACGGTAACGGTATTGAAGAGAATGCTTGACACGCATTGAAGAGAATGCTTGACAClick to see list of reads 26,005,090 - 26,005,299 26,005,094 - 26,005,303 26,005,096 - 26,005,305 26,005,097 - 26,005,306 26,005,215 - 26,005,424 26,005,312 - 26,005,521 26,005,482 - 26,005,691 26,005,491 - 26,005,700 26,005,739 - 26,005,948 26,005,800 - 26,006,009 26,005,870 - 26,006,079 26,005,892 - 26,006,101 26,006,000 - 26,006,209 26,006,016 - 26,006,225 26,006,310 - 26,006,519 26,006,468 - 26,006,677 26,006,551 - 26,006,760 26,006,565 - 26,006,774 26,006,629 - 26,006,838 26,006,707 - 26,006,916 26,006,930 - 26,007,139 26,007,105 - 26,007,314 26,007,361 - 26,007,570 26,008,650 - 26,008,441 26,008,616 - 26,008,407 26,008,436 - 26,008,227 26,008,360 - 26,008,151 26,007,755 - 26,007,546 26,007,574 - 26,007,365 26,007,418 - 26,007,209 26,007,405 - 26,007,196 26,007,287 - 26,007,078 26,006,947 - 26,006,738 26,006,881 - 26,006,672 26,006,751 - 26,006,542 26,006,750 - 26,006,541 26,006,741 - 26,006,532 26,006,740 - 26,006,531 26,006,738 - 26,006,529 26,006,717 - 26,006,508 26,006,619 - 26,006,410 26,006,570 - 26,006,361 26,005,858 - 26,005,649 26,005,575 - 26,005,366 26,005,573 - 26,005,364 26,005,482 - 26,005,273 26,005,266 - 26,005,057 26,005,263 - 26,005,054 26,005,201 - 26,004,992 26,005,087 - 26,004,878 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
AT1G69170 1 w protein-coding 26,005,068 26,007,263 1 No splice variant annotated
    Predicted function: Squamosa promoter-binding protein-like (SBP domain) transcription factor family protein