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.
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 |
|---|---|---|---|---|---|---|---|
| AT4G04408 | 4 | c | protein-coding This gene is annotated as a pseudogene |
2,184,400 | 2,184,059 | 1 | No splice variant annotated |
| Predicted function: | |||||||
- Extract sequence for this gene
- View the following for this gene:
- Go to chromosome viewer for region around this gene
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