Table 1.

Over–represented Gene Ontology (GO) terms of top 1,000 intron retention (IR) genes regulated by red and blue light

Red light
GO term	P value
MF: structural constituent of ribosome	3.95E–29
CC: ribosome	9.50E–25
BP: translation	1.22E–22
CC: integral to membrane	1.19E–06
BP: cell redox homeostasis	1.96E–06
CC: mitochondrion	8.95E–05
MF: glycerone kinase activity	9.31E–05
A total of 1,000 genes were submitted to the GOBU functional enrichment tool, which resulted in 689 unique genes with annotations. Terms are ranked by P value of over–representation and are included in list if P <1E–04. BP: Biological process; CC: Cellular component; MF: Molecular function.
Blue light
GO term	P value
CC: chloroplast	4.67E–33
MF: structural constituent of ribosome	1.66E–29
CC: ribosome	5.14E–27
BP: translation	1.63E–20
BP: reductive pentose–phosphate cycle	1.47E–16
CC: photosystem II	2.36E–10
BP: photosynthesis, light harvesting	6.62E–10
CC: photosystem I	8.56E–10
CC: stromule	2.32E–09
MF: chlorophyll binding	2.53E–08
CC: thylakoid	6.47E–08
BP: photorespiration	1.00E–07
CC: chloroplast envelope	1.12E–07
BP: photosynthesis	3.92E–07
CC: oxygen evolving complex	5.16E–07
CC: cytosolic ribosome	3.22E–06
MF: rRNA binding	1.68E–05
BP: cell redox homeostasis	2.21E–05
BP: translational elongation	2.26E–05
MF: ribulose–bisphosphate carboxylase activity	2.86E–05
BP: nitrate assimilation	5.10E–05
MF: glycerone kinase activity	7.63E–05

A total of 1,000 genes were submitted to the GOBU functional enrichment tool, which resulted in 733 unique genes with annotations. Terms are ranked by P value of over–representation and are included in list if P <1E–04.

BP: Biological process; CC: Cellular component; MF: Molecular function.