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Search Condition : Filter((traitClassFacetEn:041_Character as QTL OR traitClassFacetEn:042_Character as QTL - Grain quality OR traitClassFacetEn:043_Character as QTL - Yield and productivity OR traitClassFacetEn:044_Character as QTL - Plant growth activity OR traitClassFacetEn:045_Character as QTL - Germination OR traitClassFacetEn:046_Character as QTL - Root activity OR traitClassFacetEn:047_Character as QTL - Seed sterility))
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CGSNL
Gene
Symbol 		Gene symbol synonym(s) CGSNL Gene Name Gene name synonym(s) Chr. No. Trait Class Gene Ontology Trait Ontology Plant Ontology RAP ID MSU ID Mutant
Image
CENH3 OsCENH3
CenH3
 CENTROMERIC HISTONE 3C centromeric histone H3
centromere-specific histone H3
centromere-specific H3 histone
centromere-specific histone H3
 5 Character as QTL - Plant growth activity
Biochemical character
Reproductive organ - Pollination, fertilization, fertility
Reproductive organ - Heading date
 GO:0006334 - nucleosome assembly
GO:0005515 - protein binding
GO:0009567 - double fertilization forming a zygote and endosperm
GO:0051983 - regulation of chromosome segregation
GO:0000776 - kinetochore
GO:0046982 - protein heterodimerization activity
GO:0003677 - DNA binding
GO:0007276 - gamete generation
GO:0030527 - structural constituent of chromatin
GO:0009960 - endosperm development
GO:0048573 - photoperiodism, flowering
GO:0009793 - embryonic development ending in seed dormancy
GO:0000775 - chromosome, centromeric region
GO:0051382 - kinetochore assembly
GO:0000786 - nucleosome
GO:0005634 - nucleus
 TO:0000040 - panicle length
TO:0002616 - flowering time
TO:0000207 - plant height
TO:0000137 - days to heading
TO:0000620 - embryo development trait
TO:0002757 - flag leaf length
TO:0000455 - seed set percent
TO:0000421 - pollen fertility
 PO:0007631 - plant embryo stage
PO:0007633 - endosperm development stage
Os05g0489800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g41080.1
LOC_Os05g41080.2
GH3-8 OsGH3-8
OsMGH3
OsGH3.8
GH3.8
OsGH3-2
 GRETCHEN HAGEN 3 GENE 8 Gretchen Hagen 3 protein 8
 7 Vegetative organ - Culm
Reproductive organ - Spikelet, flower, glume, awn
Tolerance and resistance - Disease resistance
Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
 GO:0009863 - salicylic acid mediated signaling pathway
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009852 - auxin catabolic process
GO:0006955 - immune response
GO:0010279 - indole-3-acetic acid amido synthetase activity
GO:0016874 - ligase activity
GO:0009651 - response to salt stress
GO:0051607 - defense response to virus
GO:0009908 - flower development
 TO:0000172 - jasmonic acid sensitivity
TO:0000207 - plant height
TO:0000622 - flower development trait
TO:0000401 - plant growth hormone sensitivity
TO:0000346 - tiller number
TO:0006001 - salt tolerance
TO:0000020 - black streak dwarf virus resistance
TO:0002672 - auxin content
 PO:0009066 - anther
PO:0005052 - plant callus
PO:0008037 - seedling
PO:0009010 - seed
PO:0009049 - inflorescence
PO:0007615 - flower development stage
Os07g0592600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g40290.1
NH1 OsNH1
OsNPR1
OsNPR1/NH1
NPR1
OsPR2
PR2
DLN5
OsDLN5
OsBTBA1
BTBA1
 NPR1 HOMOLOG 1 NPR1-like 1
NPR1 homologue 1
nonexpresser of PR genes 1
Arabidopsis NPR1 homolog 1
non-expressor of pathogenesis-related gene 1
Arabidopsis NPR1 homologue 1
pathogenesis-related gene 2
nonexpressor of PR genes 1
Nonexpressor of Pathogenesis-Related Genes1
NONEXPRESSOR OF PATHOGENESIS-RELATED1 HOMOLOG1
NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1
non-expressor pathogenesis-related 1
NONEXPRESSOR OF PR1
DLN repressor 5
DLN motif protein 5
BTB-type E3 ubiquitin ligase A1
 1 Tolerance and resistance - Insect resistance
Vegetative organ - Culm
Tolerance and resistance - Lesion mimic
Character as QTL - Yield and productivity
Vegetative organ - Root
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0010200 - response to chitin
GO:0009734 - auxin mediated signaling pathway
GO:0008219 - cell death
GO:0051607 - defense response to virus
GO:0005829 - cytosol
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0009609 - response to symbiotic bacterium
GO:0006952 - defense response
GO:0048364 - root development
GO:0010942 - positive regulation of cell death
GO:0006950 - response to stress
GO:0031348 - negative regulation of defense response
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0009625 - response to insect
GO:0016563 - transcription activator activity
GO:0009863 - salicylic acid mediated signaling pathway
GO:0002237 - response to molecule of bacterial origin
GO:0042742 - defense response to bacterium
GO:0009737 - response to abscisic acid stimulus
GO:0005634 - nucleus
GO:0002213 - defense response to insect
GO:0009814 - defense response, incompatible interaction
GO:0002215 - defense response to nematode
GO:0010112 - regulation of systemic acquired resistance
GO:0050832 - defense response to fungus
GO:0009682 - induced systemic resistance
GO:0009408 - response to heat
GO:0009611 - response to wounding
GO:0009627 - systemic acquired resistance
 TO:0000424 - brown planthopper resistance
TO:0000172 - jasmonic acid sensitivity
TO:0000346 - tiller number
TO:0000255 - sheath blight disease resistance
TO:0000074 - blast disease
TO:0000181 - seed weight
TO:0000207 - plant height
TO:0000615 - abscisic acid sensitivity
TO:0000112 - disease resistance
TO:0000401 - plant growth hormone sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000384 - nematode damage resistance
TO:0000656 - root development trait
TO:0000445 - seed number
TO:0000148 - viral disease resistance
TO:0000163 - auxin sensitivity
TO:0000063 - mimic response
 PO:0007089 - stem elongation stage
PO:0007520 - root development stage
Os01g0194300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g09800.1
CIPK01 OsCIPK01
CIPK1
OsCIPK1
OsSnRK3.3
SnRK3.3
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 1 CBL-interacting protein kinase 1
Sucrose nonfermenting-1-related protein kinase 3.3
 1 Seed - Morphological traits - Grain shape
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Biochemical character
Character as QTL - Yield and productivity
 GO:0009409 - response to cold
GO:0004674 - protein serine/threonine kinase activity
GO:0005524 - ATP binding
GO:0004713 - protein tyrosine kinase activity
GO:0030307 - positive regulation of cell growth
GO:0009740 - gibberellic acid mediated signaling
GO:0009413 - response to flooding
GO:0009651 - response to salt stress
GO:0030145 - manganese ion binding
GO:0006468 - protein amino acid phosphorylation
GO:0007165 - signal transduction
GO:0009414 - response to water deprivation
 TO:0000303 - cold tolerance
TO:0000382 - 1000-seed weight
TO:0000432 - temperature response trait
TO:0020033 - glume length
TO:0020034 - glume width
TO:0000734 - grain length
TO:0000207 - plant height
TO:0002675 - gibberellic acid content
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000396 - grain yield
TO:0000391 - seed size
TO:0000397 - grain size
TO:0000590 - grain weight
TO:0000114 - flooding related trait
 PO:0025034 - leaf
Os01g0292200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g18800.3
LOC_Os01g18800.4
LOC_Os01g18800.1
LOC_Os01g18800.2
LOC_Os01g18800.5
CIPK02 OsCIPK02
CIPK2
OsCIPK2
OsSnRK3.26
SnRK3.26
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 2 CBL-interacting protein kinase 2
Sucrose nonfermenting-1-related protein kinase 3.26
 7 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Vegetative organ - Root
 GO:0015770 - sucrose transport
GO:0034219 - carbohydrate transmembrane transport
GO:0009409 - response to cold
GO:0009737 - response to abscisic acid stimulus
GO:0005524 - ATP binding
GO:0042128 - nitrate assimilation
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0031667 - response to nutrient levels
GO:0004674 - protein serine/threonine kinase activity
GO:0006995 - cellular response to nitrogen starvation
GO:0042594 - response to starvation
GO:0019740 - nitrogen utilization
GO:0006468 - protein amino acid phosphorylation
GO:0007165 - signal transduction
GO:0009651 - response to salt stress
GO:0044136 - development of symbiont on or near host rhizosphere
GO:0030145 - manganese ion binding
 TO:0000371 - yield trait
TO:0001027 - net photosynthetic rate
TO:0000495 - chlorophyll content
TO:0000644 - relative root dry weight
TO:0000636 - relative shoot dry weight
TO:0000455 - seed set percent
TO:0000152 - panicle number
TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000291 - carbohydrate content
TO:0000011 - nitrogen sensitivity
TO:0000382 - 1000-seed weight
TO:0000449 - grain yield per plant
TO:0000128 - harvest index
 PO:0009005 - root
Os07g0678600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g48100.1
CIPK17 OsCIPK17
OsSnRK3.14
SnRK3.14
 CALCINEURIN B-LIKE PROTEIN-INTERACTING PROTEIN KINASE 17 CBL-interacting protein kinase 17
Sucrose nonfermenting-1-related protein kinase 3.14
 5 Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Vegetative organ - Root
Tolerance and resistance - Disease resistance
Character as QTL - Plant growth activity
Character as QTL - Germination
Biochemical character
 GO:0046686 - response to cadmium ion
GO:0009414 - response to water deprivation
GO:0009409 - response to cold
GO:0004674 - protein serine/threonine kinase activity
GO:0007165 - signal transduction
GO:0006952 - defense response
GO:0005737 - cytoplasm
GO:0009408 - response to heat
GO:0010187 - negative regulation of seed germination
GO:0009651 - response to salt stress
GO:0006468 - protein amino acid phosphorylation
GO:0005524 - ATP binding
GO:0030145 - manganese ion binding
 TO:0000112 - disease resistance
TO:0000259 - heat tolerance
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000303 - cold tolerance
TO:0000352 - plant dry weight
TO:0000578 - root fresh weight
TO:0000227 - root length
TO:0000207 - plant height
 PO:0009005 - root
Os05g0136200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g04550.1
DMI3 OsDMI3
OsCCaMK1
OsCCaMK
OsCCAMK
CCAMK
 DOESN'T MAKE INFECTIONS 3 DOESN'T MAKE INFECTIONS3
calcium and calmodulin-dependent protein kinase 1
Ca2+/calmodulin (CaM)-dependent protein kinase
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE
 5 Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Character as QTL - Germination
 GO:0009610 - response to symbiotic fungus
GO:0005737 - cytoplasm
GO:0005634 - nucleus
GO:0009734 - auxin mediated signaling pathway
GO:0009651 - response to salt stress
GO:0048364 - root development
GO:0019722 - calcium-mediated signaling
GO:0010726 - positive regulation of hydrogen peroxide metabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0005524 - ATP binding
GO:0005509 - calcium ion binding
GO:0006979 - response to oxidative stress
GO:0009789 - positive regulation of abscisic acid mediated signaling
GO:0010030 - positive regulation of seed germination
GO:0050832 - defense response to fungus
GO:0047484 - regulation of response to osmotic stress
GO:0006970 - response to osmotic stress
GO:0018107 - peptidyl-threonine phosphorylation
GO:0060267 - positive regulation of respiratory burst
GO:0030104 - water homeostasis
GO:0044403 - symbiosis, encompassing mutualism through parasitism
GO:0042542 - response to hydrogen peroxide
GO:0010729 - positive regulation of hydrogen peroxide biosynthetic process
GO:0004683 - calmodulin-dependent protein kinase activity
GO:0043408 - regulation of MAPKKK cascade
GO:0009738 - abscisic acid mediated signaling
GO:0009845 - seed germination
GO:0009414 - response to water deprivation
GO:0016021 - integral to membrane
 TO:0000615 - abscisic acid sensitivity
TO:0000656 - root development trait
TO:0002657 - oxidative stress
TO:0000136 - relative water content
TO:0000074 - blast disease
TO:0000605 - hydrogen peroxide content
TO:0000095 - osmotic response sensitivity
TO:0006001 - salt tolerance
TO:0000516 - relative root length
TO:0000276 - drought tolerance
TO:0002672 - auxin content
 PO:0007520 - root development stage
PO:0007057 - 0 seed germination stage
Os05g0489900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g41090.1
MADS51 OsMADS51
OsMADS65
MADS65
qHd1
DLN36
OsDLN36
 MADS BOX GENE 51 MADS box gene51
DLN repressor 36
DLN motif protein 36
 1 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Tolerance and resistance - Stress tolerance
Seed - Morphological traits
Character as QTL - Plant growth activity
Other
Tolerance and resistance - Disease resistance
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009408 - response to heat
GO:0050832 - defense response to fungus
GO:0009409 - response to cold
GO:0043565 - sequence-specific DNA binding
 TO:0000396 - grain yield
TO:0000259 - heat tolerance
TO:0000432 - temperature response trait
TO:0000137 - days to heading
TO:0002616 - flowering time
TO:0000449 - grain yield per plant
TO:0000152 - panicle number
TO:0000455 - seed set percent
TO:0000329 - tillering ability
TO:0000357 - growth and development trait
TO:0000074 - blast disease
TO:0000590 - grain weight
TO:0000303 - cold tolerance
 Os01g0922800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g69850.1
MIR156B miR156b
OsmiR156b
osmiR156b
osa-miR156b
osa-MIR156b
miR156b*osa-miR156b-3p osa-miR156b-5p
 MICRORNA156B micro RNA 156b
microRNA156b
osa-miRNA156b
 1 Tolerance and resistance - Disease resistance
Other
Character as QTL - Plant growth activity
 GO:0050832 - defense response to fungus
GO:0006379 - mRNA cleavage
GO:0016442 - RNA-induced silencing complex
GO:0035068 - micro-ribonucleoprotein complex
GO:0035195 - gene silencing by miRNA
GO:0010050 - vegetative phase change
GO:0032350 - regulation of hormone metabolic process
 TO:0000357 - growth and development trait
TO:0000074 - blast disease
TO:0000476 - growth hormone content
 PO:0009005 - root
PO:0009049 - inflorescence
PO:0000009 - cultured plant callus
PO:0009025 - vascular leaf
-
SDT miR156h
OsmiR156h
osmiR156h
osa-miR156h
osa-MIR156hosa-miR156h-3p osa-miR156h-5p
 SEMIDWARF AND HIGH-TILLERING micro RNA 156h
microRNA156h
osa-miRNA156h
semidwarf and high-tillering
 6 Tolerance and resistance - Stress tolerance
Other
Character as QTL - Yield and productivity
Vegetative organ - Culm
Tolerance and resistance - Disease resistance
 GO:0007623 - circadian rhythm
GO:0050832 - defense response to fungus
GO:0006379 - mRNA cleavage
GO:0016442 - RNA-induced silencing complex
GO:0035068 - micro-ribonucleoprotein complex
GO:0035195 - gene silencing by miRNA
 TO:0000050 - inflorescence branching
TO:0000074 - blast disease
TO:0000207 - plant height
TO:0000329 - tillering ability
TO:0000068 - lodging incidence
TO:0000346 - tiller number
TO:0000396 - grain yield
 PO:0000009 - cultured plant callus
PO:0009005 - root
PO:0009025 - vascular leaf
PO:0009049 - inflorescence
-
YUCCA1 OsYUCCA1
OsYUC1
YUC1
 YUCCA-LIKE GENE 1 (YUCCA-like gene)
 1 Tolerance and resistance - Disease resistance
Vegetative organ - Root
Character as QTL - Yield and productivity
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0010229 - inflorescence development
GO:0048364 - root development
GO:0009609 - response to symbiotic bacterium
GO:0051607 - defense response to virus
GO:0034059 - response to anoxia
GO:0009737 - response to abscisic acid stimulus
GO:0004499 - flavin-containing monooxygenase activity
GO:0009851 - auxin biosynthetic process
GO:0046686 - response to cadmium ion
GO:0046685 - response to arsenic
GO:0048830 - adventitious root development
GO:0009408 - response to heat
GO:0009414 - response to water deprivation
 TO:0000396 - grain yield
TO:0000031 - silicon sensitivity
TO:0000227 - root length
TO:0000020 - black streak dwarf virus resistance
TO:0000084 - root number
TO:0000656 - root development trait
TO:0000428 - callus induction
TO:0000615 - abscisic acid sensitivity
TO:0000447 - filled grain number
TO:0000259 - heat tolerance
TO:0000276 - drought tolerance
TO:0002672 - auxin content
TO:0000578 - root fresh weight
TO:0000621 - inflorescence development trait
TO:0001013 - lateral root number
TO:0000557 - secondary branch number
TO:0001006 - adventitious root number
TO:0000449 - grain yield per plant
 PO:0020103 - flag leaf
PO:0009105 - inflorescence branch meristem
Os01g0645400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g45760.1
LOC_Os01g45760.2
RBOHB rbohB
OsrbohB
Os rbohB
OsRbohB
OsNox1
Nox1
Os-RbohB
RbohB
OsRboh1
Rboh1
 RESPIRATORY BURST OXIDASE HOMOLOG B Respiratory Burst Oxidase Homolog B
Respiratory Burst Oxidase Homologue B
NADPH oxidase 1
 1 Biochemical character
Vegetative organ - Root
Reproductive organ - Pollination, fertilization, fertility
Character as QTL - Germination
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
 GO:0009687 - abscisic acid metabolic process
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0009751 - response to salicylic acid stimulus
GO:0004601 - peroxidase activity
GO:0005509 - calcium ion binding
GO:0009408 - response to heat
GO:0009734 - auxin mediated signaling pathway
GO:0009845 - seed germination
GO:0006952 - defense response
GO:0009626 - plant-type hypersensitive response
GO:0030104 - water homeostasis
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0002238 - response to molecule of fungal origin
GO:0009753 - response to jasmonic acid stimulus
GO:0005886 - plasma membrane
GO:0010266 - response to vitamin B1
GO:0050832 - defense response to fungus
GO:0009737 - response to abscisic acid stimulus
GO:0043621 - protein self-association
GO:0009733 - response to auxin stimulus
GO:0050665 - hydrogen peroxide biosynthetic process
GO:0006970 - response to osmotic stress
GO:0009413 - response to flooding
GO:0048364 - root development
GO:0006979 - response to oxidative stress
GO:0016174 - NAD(P)H oxidase activity
GO:0002679 - respiratory burst during defense response
GO:0009738 - abscisic acid mediated signaling
GO:0016021 - integral to membrane
GO:0009566 - fertilization
GO:0010118 - stomatal movement
GO:0043020 - NADPH oxidase complex
GO:0042742 - defense response to bacterium
 TO:0000112 - disease resistance
TO:0000605 - hydrogen peroxide content
TO:0000175 - bacterial blight disease resistance
TO:0000656 - root development trait
TO:0002657 - oxidative stress
TO:0006002 - proline content
TO:0000276 - drought tolerance
TO:0000163 - auxin sensitivity
TO:0000074 - blast disease
TO:0000439 - fungal disease resistance
TO:0000136 - relative water content
TO:0000172 - jasmonic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000524 - submergence tolerance
TO:0006001 - salt tolerance
TO:0002667 - abscisic acid content
TO:0000095 - osmotic response sensitivity
TO:0000129 - false smut disease resistance
TO:0000520 - stomatal closure rate
TO:0000430 - germination rate
TO:0000382 - 1000-seed weight
 PO:0025034 - leaf
Os01g0360200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g25820.2
LOC_Os01g25820.1
FLO27 OsbZIP58
bZIP58
OsEnS-92
OsSMF1
SMF1
OsRISBZ1
RISBZ1/bZIP58
RISBZ1
OsFLO27
 FLOURY ENDOSPERM 27 bZIP transcription factor 58
rice seed b-Zipper 1
endosperm-specific gene 92
seed maturation factor 1
rice seed basic leucine zipper 1
RICE SEED bZIP1
 7 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Seed - Morphological traits - Grain shape
Seed - Morphological traits - Endosperm
Other
 GO:0034976 - response to endoplasmic reticulum stress
GO:0009408 - response to heat
GO:0009845 - seed germination
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010581 - regulation of starch biosynthetic process
GO:0009960 - endosperm development
GO:0012501 - programmed cell death
GO:0010431 - seed maturation
GO:0043565 - sequence-specific DNA binding
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0030968 - endoplasmic reticulum unfolded protein response
 TO:0002653 - endosperm storage protein content
TO:0002661 - seed maturation
TO:0000104 - floury endosperm
TO:0000432 - temperature response trait
TO:0000259 - heat tolerance
TO:0002673 - amino acid content
TO:0000590 - grain weight
TO:0000399 - grain thickness
TO:0000402 - grain width
TO:0000734 - grain length
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0002656 - starch grain shape
TO:0000100 - shrunken endosperm
TO:0000487 - endosperm color
TO:0000490 - protein composition related trait
 PO:0007057 - 0 seed germination stage
PO:0007632 - seed maturation stage
PO:0009089 - endosperm
PO:0005360 - aleurone layer
PO:0007633 - endosperm development stage
Os07g0182000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g08420.1
AMY1A Amy1A/C*(RAmy1A/C)
alpha Amy7
AMY1.1
Amy1A
RAmy1A/C
Amy1A/C*
Amy1
Amy1A_C
OsAmy1A
alphaAmy7-C
RAmy1A
AmyI-1
OsAmyI-1
OsRamy1A
RAmy1A
 ALPHA-AMYLASE 1A Alpha-amylase1A
Alpha-amylase-1A
Alpha-amylase isozyme 1B
Amylase-1
alpha-amylase I-1
 2 Character as QTL - Grain quality
Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Germination
 GO:0010353 - response to trehalose stimulus
GO:0010030 - positive regulation of seed germination
GO:0009409 - response to cold
GO:0009651 - response to salt stress
GO:0009737 - response to abscisic acid stimulus
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0004556 - alpha-amylase activity
GO:0010182 - sugar mediated signaling
GO:0005983 - starch catabolic process
GO:0009739 - response to gibberellin stimulus
GO:0005987 - sucrose catabolic process
GO:0009408 - response to heat
GO:0005509 - calcium ion binding
GO:0010212 - response to ionizing radiation
 TO:0000166 - gibberellic acid sensitivity
TO:0000161 - radiation response trait
TO:0006001 - salt tolerance
TO:0000303 - cold tolerance
TO:0000266 - chalky endosperm
TO:0000409 - peak viscosity
TO:0000483 - germinability at low temperature
TO:0000259 - heat tolerance
TO:0002694 - fruit flavor trait
TO:0000615 - abscisic acid sensitivity
 PO:0001170 - seed development stage
PO:0007633 - endosperm development stage
PO:0009010 - seed
Os02g0765600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g52710.1
AMY1C Amy1A/C*(RAmy1A/C)
alpha Amy10
Amy1C
RAmy1A/C
Amy1A/C*
Amy3
RAmy1C
OsAmy1C
alphaAmy10-C
OsRAmy3A
RAmy3A
 ALPHA-AMYLASE 1C Alpha-amylase1C
Alpha-amylase 1C
Amylase-3
Alpha-amylase-1A
alpha-amylase 10-C
 2 Seed - Physiological traits - Dormancy
Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
Character as QTL - Germination
 GO:0009737 - response to abscisic acid stimulus
GO:0004556 - alpha-amylase activity
GO:0005983 - starch catabolic process
GO:0005975 - carbohydrate metabolic process
GO:0005509 - calcium ion binding
GO:0009651 - response to salt stress
GO:0009845 - seed germination
GO:0009408 - response to heat
 TO:0006001 - salt tolerance
TO:0000259 - heat tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000266 - chalky endosperm
 PO:0009010 - seed
PO:0007633 - endosperm development stage
PO:0007057 - 0 seed germination stage
Os02g0765400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g52700.1
ESL4 CDPK12
OsCDPK12
OsCPK12
CPK12
OsESL4
 EARLY SENESCENCE LEAF 4 calcium-dependent protein kinase
Calcium-dependent protein kinase 12
Early senescence leaf 4
 4 Biochemical character
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Tolerance and resistance
Character as QTL - Plant growth activity
Vegetative organ - Leaf
 GO:0005634 - nucleus
GO:0016020 - membrane
GO:0009414 - response to water deprivation
GO:0005509 - calcium ion binding
GO:0005524 - ATP binding
GO:0004674 - protein serine/threonine kinase activity
GO:0031000 - response to caffeine
GO:0005737 - cytoplasm
GO:0005886 - plasma membrane
GO:0009627 - systemic acquired resistance
GO:0009697 - salicylic acid biosynthetic process
GO:0006979 - response to oxidative stress
GO:0018105 - peptidyl-serine phosphorylation
GO:0010310 - regulation of hydrogen peroxide metabolic process
GO:0006807 - nitrogen compound metabolic process
GO:0010150 - leaf senescence
 TO:0000371 - yield trait
TO:0000495 - chlorophyll content
TO:0000440 - grain number per plant
TO:0000276 - drought tolerance
TO:0000271 - inflorescence length
TO:0000605 - hydrogen peroxide content
TO:0002657 - oxidative stress
TO:0000455 - seed set percent
TO:0000249 - leaf senescence
 PO:0007633 - endosperm development stage
PO:0020104 - leaf sheath
PO:0009047 - stem
PO:0025034 - leaf
Os04g0560600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g47300.1
AMY3C Amy3A/B/C*(RAmy3A/B/C)
AmyII-6
AMY1.7
Amy3C
RAmy3A/B/C
Amy3A/B/C*
Amy7
AMY3B
RAmy3C
OsAmy3B
 ALPHA-AMYLASE 3C Alpha-amylase3C
Alpha-amylase isozyme 3C precursor
Alpha-amylase isozyme 3C
Amylase-7
Alpha-amylase-3A
 9 Character as QTL - Germination
Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Dormancy
 GO:0009739 - response to gibberellin stimulus
GO:0005509 - calcium ion binding
GO:0009737 - response to abscisic acid stimulus
GO:0004556 - alpha-amylase activity
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0005987 - sucrose catabolic process
GO:0005983 - starch catabolic process
GO:0005975 - carbohydrate metabolic process
GO:0009845 - seed germination
GO:0009408 - response to heat
 TO:0000259 - heat tolerance
TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
 PO:0007057 - 0 seed germination stage
Os09g0457800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g28420.1
CATA CATA1
Cat A1*
OSCAT-A
Cat2
CatA1
CAT-A
OsCatA
OsCAT
CAT
catA
OSCATA
OsCATc
OsCATA
OsCAT1A
CAT1
OsCAT1
OsCATC
OsCAT2
 CATALASE A CATALASE A
Catalase-2*
Catalase-Al (cDNA clone)
Catalase isozyme A
 2 Biochemical character
Tolerance and resistance - Disease resistance
Character as QTL - Germination
Tolerance and resistance - Stress tolerance
Character as QTL - Plant growth activity
Character as QTL - Yield and productivity
 GO:0009609 - response to symbiotic bacterium
GO:0005634 - nucleus
GO:0043067 - regulation of programmed cell death
GO:0009737 - response to abscisic acid stimulus
GO:0009514 - glyoxysome
GO:0042542 - response to hydrogen peroxide
GO:0006979 - response to oxidative stress
GO:0009408 - response to heat
GO:0009409 - response to cold
GO:0004096 - catalase activity
GO:0042744 - hydrogen peroxide catabolic process
GO:0055114 - oxidation reduction
GO:0042742 - defense response to bacterium
GO:0010446 - response to alkalinity
GO:0009845 - seed germination
GO:0005737 - cytoplasm
GO:0009725 - response to hormone stimulus
GO:0009738 - abscisic acid mediated signaling
GO:0009739 - response to gibberellin stimulus
GO:0009651 - response to salt stress
GO:0005829 - cytosol
GO:0005777 - peroxisome
GO:0006801 - superoxide metabolic process
GO:0051775 - response to redox state
GO:0020037 - heme binding
GO:0009751 - response to salicylic acid stimulus
GO:0010332 - response to gamma radiation
GO:0009414 - response to water deprivation
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0010029 - regulation of seed germination
 TO:0000207 - plant height
TO:0001016 - relative chlorophyll content
TO:0000136 - relative water content
TO:0000382 - 1000-seed weight
TO:0000031 - silicon sensitivity
TO:0000326 - leaf color
TO:0000303 - cold tolerance
TO:0000175 - bacterial blight disease resistance
TO:0000259 - heat tolerance
TO:0000166 - gibberellic acid sensitivity
TO:0000455 - seed set percent
TO:0000615 - abscisic acid sensitivity
TO:0000152 - panicle number
TO:0000276 - drought tolerance
TO:0006001 - salt tolerance
TO:0002657 - oxidative stress
TO:0000401 - plant growth hormone sensitivity
TO:0000481 - alkali sensitivity
TO:0000605 - hydrogen peroxide content
 PO:0009047 - stem
PO:0009010 - seed
PO:0009066 - anther
PO:0007022 - seed imbibition stage
PO:0007057 - 0 seed germination stage
PO:0025034 - leaf
Os02g0115700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g02400.2
LOC_Os02g02400.3
LOC_Os02g02400.1
SSIIIB OsSSIIIb. SSIII-1
SSIIIa
 SOLUBLE STARCH SYNTHASE IIIB 4 Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
Character as QTL - Yield and productivity
Biochemical character
Seed - Physiological traits - Storage substances
 GO:0009011 - starch synthase activity
GO:0009501 - amyloplast
GO:0019252 - starch biosynthetic process
GO:0010229 - inflorescence development
GO:0009507 - chloroplast
GO:0009408 - response to heat
 TO:0000396 - grain yield
TO:0000259 - heat tolerance
TO:0000604 - fat and essential oil content
TO:0000196 - amylose content
TO:0000382 - 1000-seed weight
TO:0000621 - inflorescence development trait
TO:0000696 - starch content
 PO:0009010 - seed
PO:0009072 - plant ovary
PO:0009009 - plant embryo
PO:0001083 - inflorescence development stage
PO:0009089 - endosperm
PO:0025034 - leaf
PO:0009049 - inflorescence
Os04g0624600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g53310.1
NOE1 CATC
OsCat
OsCatC
OsCATC
OsNOE1
noe1
catC
OsCATC
CAT3
OsCAT3
LLM9428
OsLLM9428
 NITRIC OXIDE EXCESS 1 catalase C
catalase isozyme C
nitric oxide excess1
large lesion mimic mutant 9428
 3 Biochemical character
Vegetative organ - Leaf
Character as QTL - Plant growth activity
Seed - Physiological traits - Shattering
Tolerance and resistance - Disease resistance
Vegetative organ - Culm
Tolerance and resistance - Lesion mimic
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
 GO:0010939 - regulation of necrotic cell death
GO:0009725 - response to hormone stimulus
GO:0042744 - hydrogen peroxide catabolic process
GO:0005982 - starch metabolic process
GO:0009409 - response to cold
GO:0050832 - defense response to fungus
GO:0009414 - response to water deprivation
GO:0009642 - response to light intensity
GO:0033484 - nitric oxide homeostasis
GO:0010229 - inflorescence development
GO:0031348 - negative regulation of defense response
GO:0042548 - regulation of photosynthesis, light reaction
GO:0005634 - nucleus
GO:0004096 - catalase activity
GO:0006979 - response to oxidative stress
GO:0042742 - defense response to bacterium
GO:0020037 - heme binding
GO:0009404 - toxin metabolic process
GO:0043067 - regulation of programmed cell death
GO:0009651 - response to salt stress
GO:0005739 - mitochondrion
GO:0006801 - superoxide metabolic process
GO:0010150 - leaf senescence
GO:0050777 - negative regulation of immune response
GO:0009737 - response to abscisic acid stimulus
GO:0009408 - response to heat
GO:0005777 - peroxisome
GO:0045454 - cell redox homeostasis
GO:0009416 - response to light stimulus
 TO:0000346 - tiller number
TO:0000207 - plant height
TO:0000074 - blast disease
TO:0000382 - 1000-seed weight
TO:0000175 - bacterial blight disease resistance
TO:0000303 - cold tolerance
TO:0000249 - leaf senescence
TO:0006001 - salt tolerance
TO:0000259 - heat tolerance
TO:0002657 - oxidative stress
TO:0000605 - hydrogen peroxide content
TO:0000063 - mimic response
TO:0000455 - seed set percent
TO:0000326 - leaf color
TO:0000019 - seedling height
TO:0002637 - leaf size
TO:0000460 - light intensity sensitivity
TO:0000075 - light sensitivity
TO:0000357 - growth and development trait
TO:0002662 - leaf rolling tolerance
TO:0000621 - inflorescence development trait
TO:0000276 - drought tolerance
TO:0000473 - grain shattering
TO:0000615 - abscisic acid sensitivity
TO:0000152 - panicle number
TO:0000401 - plant growth hormone sensitivity
TO:0000447 - filled grain number
 PO:0001054 - 4 leaf senescence stage
PO:0025034 - leaf
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0001083 - inflorescence development stage
Os03g0131200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g03910.1
GHD7 Ghd2
Ghd7
OsGhd7
OsCCT26
OsCMF8
OsI
Ghd7/Hd4
Hd4
EH7-1/Hd4
Ghd7-0a
EH7-1
EH7/Ghd7
EH7
OsEH7
GLW7.1
OsGLW7.1
 HEADING DATE 7 heading date 7
"Grain number
plant height
and heading date7"
"GRAIN NUMBER
PLANT HEIGHT AND HEADING DATE 7"
CCT domain-containing gene 26
CCT (CO, CO-LIKE and TOC1) domain protein 26
CCT domain protein 26
CCT MOTIF FAMILY (CMF) gene 8
Early heading 7
"Grain Length
Width and Weight 7.1"
Grain height date 7
 7 Character as QTL - Yield and productivity
Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Heterochrony
Seed - Physiological traits
Vegetative organ - Culm
Seed - Physiological traits - Storage substances
Seed - Physiological traits - Taste
 GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009648 - photoperiodism
GO:0005985 - sucrose metabolic process
GO:0042128 - nitrate assimilation
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0045848 - positive regulation of nitrogen utilization
GO:0006521 - regulation of cellular amino acid metabolic process
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0008643 - carbohydrate transport
GO:0048573 - photoperiodism, flowering
GO:0051781 - positive regulation of cell division
GO:0009416 - response to light stimulus
GO:0009740 - gibberellic acid mediated signaling
GO:0010229 - inflorescence development
GO:0007623 - circadian rhythm
GO:0030307 - positive regulation of cell growth
GO:0006109 - regulation of carbohydrate metabolic process
GO:0015770 - sucrose transport
GO:0006808 - regulation of nitrogen utilization
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0010109 - regulation of photosynthesis
GO:0009744 - response to sucrose stimulus
GO:0009745 - sucrose mediated signaling
 TO:0000621 - inflorescence development trait
TO:0000397 - grain size
TO:0000382 - 1000-seed weight
TO:0000734 - grain length
TO:0002653 - endosperm storage protein content
TO:0000590 - grain weight
TO:0002675 - gibberellic acid content
TO:0000266 - chalky endosperm
TO:0000469 - days to maturity
TO:0000456 - spikelet number
TO:0000229 - photoperiod sensitivity
TO:0000207 - plant height
TO:0000447 - filled grain number
TO:0000557 - secondary branch number
TO:0000050 - inflorescence branching
TO:0002759 - grain number
TO:0000011 - nitrogen sensitivity
TO:0000196 - amylose content
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0000152 - panicle number
TO:0000696 - starch content
TO:0000107 - endosperm storage protein-1 content
TO:0000109 - endosperm storage protein-2 content
TO:0000137 - days to heading
TO:0000019 - seedling height
TO:0000211 - gel consistency
TO:0002616 - flowering time
TO:0000710 - globulin protein content
TO:0000449 - grain yield per plant
TO:0000352 - plant dry weight
TO:0002680 - albumin content
TO:0000357 - growth and development trait
 PO:0001083 - inflorescence development stage
Os07g0261200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g15770.1
GIF1 gif1
CIN2
OsCIN2
OsGIF1
WB1
OsWB1
GIF1/OsCIN2
 GRAIN INCOMPLETE FILLING 1 grain incomplete filling 1
"Beta-fructofuranosidase
insoluble isoenzyme 2"
Sucrose hydrolase 2
Invertase 2
Cell wall beta-fructosidase 2
cell-wall invertase 2
White Belly 1
 4 Seed - Morphological traits
Tolerance and resistance - Stress tolerance
Character as QTL - Yield and productivity
Seed - Physiological traits - Taste
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Morphological traits - Endosperm
 GO:0005987 - sucrose catabolic process
GO:0016787 - hydrolase activity
GO:0048046 - apoplast
GO:0051707 - response to other organism
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0005986 - sucrose biosynthetic process
GO:0004564 - beta-fructofuranosidase activity
GO:0004575 - sucrose alpha-glucosidase activity
GO:0005618 - cell wall
GO:0005975 - carbohydrate metabolic process
GO:0009960 - endosperm development
 TO:0000696 - starch content
TO:0000734 - grain length
TO:0000097 - amylopectin content
TO:0000382 - 1000-seed weight
TO:0000447 - filled grain number
TO:0000456 - spikelet number
TO:0000328 - sucrose content
TO:0000391 - seed size
TO:0000455 - seed set percent
TO:0000300 - glucose content
TO:0000311 - invertase activity
TO:0000221 - glume color
TO:0002656 - starch grain shape
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000162 - seed quality
TO:0000396 - grain yield
TO:0000397 - grain size
TO:0006005 - fructose content
TO:0000592 - 1000-dehulled grain weight
TO:0000196 - amylose content
TO:0000590 - grain weight
TO:0002661 - seed maturation
TO:0000266 - chalky endosperm
TO:0000575 - endosperm related trait
TO:0000487 - endosperm color
 PO:0005019 - carpel vascular system
PO:0009089 - endosperm
PO:0009084 - pericarp
PO:0007633 - endosperm development stage
PO:0006326 - inflorescence internode
PO:0000025 - root tip
Os04g0413500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g33740.1
HK5 OHK3
HK
OsHK5
Crl3
Ohk3
OsHK2
 HISTIDINE KINASE 5 histidine kinase 5
His kinase 5
 10 Reproductive organ - Pollination, fertilization, fertility
Reproductive organ - Heading date
Character as QTL - Plant growth activity
Biochemical character
 GO:0000156 - two-component response regulator activity
GO:0000155 - two-component sensor activity
GO:0009884 - cytokinin receptor activity
GO:0048831 - regulation of shoot development
GO:0005524 - ATP binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0016020 - membrane
GO:0018106 - peptidyl-histidine phosphorylation
GO:0048573 - photoperiodism, flowering
GO:0009735 - response to cytokinin stimulus
GO:0048364 - root development
GO:0004673 - protein histidine kinase activity
GO:0009909 - regulation of flower development
GO:0009736 - cytokinin mediated signaling
 TO:0000656 - root development trait
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000370 - leaf width
TO:0000654 - shoot development trait
TO:0000137 - days to heading
TO:0000357 - growth and development trait
TO:0000167 - cytokinin sensitivity
TO:0000622 - flower development trait
TO:0002616 - flowering time
TO:0000152 - panicle number
TO:0000485 - sterility related trait
 Os10g0362300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g21810.1
LOC_Os10g21810.2
PAL1 HK4
OHK4
HK
OsHK4
Crl1b
Ohk4
OHK4/OsHK4
OsPAL1
 PANICLE LENGTH 1 histidine kinase 4
His kinase 4
panicle length1
 3 Reproductive organ - Inflorescence
Biochemical character
Reproductive organ - panicle
Character as QTL - Plant growth activity
 GO:0009735 - response to cytokinin stimulus
GO:0000155 - two-component sensor activity
GO:0009736 - cytokinin mediated signaling
GO:0010081 - regulation of inflorescence meristem growth
GO:0009823 - cytokinin catabolic process
GO:0009691 - cytokinin biosynthetic process
GO:0000156 - two-component response regulator activity
GO:0004673 - protein histidine kinase activity
GO:0005524 - ATP binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0005886 - plasma membrane
GO:0009884 - cytokinin receptor activity
GO:0010075 - regulation of meristem growth
GO:0010229 - inflorescence development
GO:0005783 - endoplasmic reticulum
GO:0080037 - negative regulation of cytokinin mediated signaling
GO:0016020 - membrane
GO:0018106 - peptidyl-histidine phosphorylation
 TO:0000040 - panicle length
TO:0002757 - flag leaf length
TO:0000346 - tiller number
TO:0000207 - plant height
TO:0000447 - filled grain number
TO:0000096 - ratooning ability
TO:0000557 - secondary branch number
TO:0006032 - panicle size
TO:0006031 - inflorescence size
TO:0002660 - cytokinin content
TO:0000621 - inflorescence development trait
TO:0000132 - basal internode diameter
TO:0002758 - flag leaf lamina width
TO:0000167 - cytokinin sensitivity
TO:0000547 - primary branch number
 PO:0001083 - inflorescence development stage
PO:0004709 - axillary bud
Os03g0717700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g50860.1
CKT1 OHK5
HK
OsHK6
HK6
Crl1a
Ohk5
OsHK1
OsCKT1
ABL1
OsABL1
 CYTOKININ TOLERANT 1 histidine kinase 6
His kinase 6
cytokinin tolerant 1
adaxial-abaxial bipolar leaf1
ADAXIAL-ABAXIAL BIPOLAR LEAF 1
 2 Vegetative organ - Leaf
Biochemical character
Reproductive organ - Heading date
Reproductive organ - Pollination, fertilization, fertility
Character as QTL - Plant growth activity
Vegetative organ - Root
 GO:0010109 - regulation of photosynthesis
GO:0048573 - photoperiodism, flowering
GO:0000155 - two-component sensor activity
GO:0048364 - root development
GO:0004673 - protein histidine kinase activity
GO:0051302 - regulation of cell division
GO:0005783 - endoplasmic reticulum
GO:0005982 - starch metabolic process
GO:0005985 - sucrose metabolic process
GO:0009735 - response to cytokinin stimulus
GO:0009736 - cytokinin mediated signaling
GO:0009884 - cytokinin receptor activity
GO:0015995 - chlorophyll biosynthetic process
GO:0018106 - peptidyl-histidine phosphorylation
GO:0043455 - regulation of secondary metabolic process
GO:0048831 - regulation of shoot development
GO:0000156 - two-component response regulator activity
GO:0048366 - leaf development
GO:0009909 - regulation of flower development
GO:0005524 - ATP binding
GO:0006355 - regulation of transcription, DNA-dependent
GO:0016020 - membrane
 TO:0000152 - panicle number
TO:0000655 - leaf development trait
TO:0001015 - photosynthetic rate
TO:0000522 - stomatal conductance
TO:0000055 - leaf lamina pubescence
TO:0000135 - leaf length
TO:0002758 - flag leaf lamina width
TO:0000399 - grain thickness
TO:0002759 - grain number
TO:0000040 - panicle length
TO:0000316 - photosynthetic ability
TO:0000656 - root development trait
TO:0000167 - cytokinin sensitivity
TO:0002637 - leaf size
TO:0000485 - sterility related trait
TO:0002616 - flowering time
TO:0000137 - days to heading
TO:0006020 - shoot apical meristem development
TO:0000654 - shoot development trait
TO:0000622 - flower development trait
TO:0000373 - inflorescence anatomy and morphology trait
TO:0000370 - leaf width
TO:0000357 - growth and development trait
 PO:0000027 - lateral root tip
PO:0005029 - root primordium
PO:0007520 - root development stage
PO:0000025 - root tip
PO:0020121 - lateral root
Os02g0738400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g50480.1
SPL17 OsCAD1
CAD1
 SPOTTED LEAF 17 spotted leaf 17
CONSTITUTIVE ACTIVE DEFENSE 1
 1 Tolerance and resistance - Lesion mimic
Character as QTL - Plant growth activity
Character as QTL - Yield and productivity
Tolerance and resistance - Disease resistance
 GO:0016020 - membrane
GO:0005634 - nucleus
GO:0009863 - salicylic acid mediated signaling pathway
GO:0042742 - defense response to bacterium
GO:0031347 - regulation of defense response
GO:0009416 - response to light stimulus
GO:0009867 - jasmonic acid mediated signaling pathway
GO:0050832 - defense response to fungus
GO:0043067 - regulation of programmed cell death
GO:0005829 - cytosol
GO:0009626 - plant-type hypersensitive response
GO:0006952 - defense response
 TO:0000074 - blast disease
TO:0002668 - jasmonic acid content
TO:0000605 - hydrogen peroxide content
TO:0000382 - 1000-seed weight
TO:0000207 - plant height
TO:0000357 - growth and development trait
TO:0000063 - mimic response
TO:0000075 - light sensitivity
TO:0000175 - bacterial blight disease resistance
TO:0000455 - seed set percent
 PO:0025034 - leaf
Os01g0748900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g54510.1
SAMDC SamDC
AdoMetDC
AdoMetDC1
OsSAMDC1
 S-ADENOSYLMETHIONINE DECARBOXYLASE S-adenosylmethionine decarboxylase
S-adenosylmethionine decarboxylase proenzyme
S-adenosylmethionine decarboxylase alpha chain
S-adenosylmethionine decarboxylase beta chain
S-adenosylmethionine decarboxylase 1
 4 Biochemical character
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
 GO:0009846 - pollen germination
GO:0009414 - response to water deprivation
GO:0004014 - adenosylmethionine decarboxylase activity
GO:0006597 - spermine biosynthetic process
GO:0008295 - spermidine biosynthetic process
GO:0009409 - response to cold
GO:0009555 - pollen development
GO:0009651 - response to salt stress
GO:0009845 - seed germination
GO:0016209 - antioxidant activity
GO:0006596 - polyamine biosynthetic process
 TO:0000207 - plant height
TO:0000346 - tiller number
TO:0000432 - temperature response trait
TO:0000276 - drought tolerance
TO:0000430 - germination rate
TO:0000449 - grain yield per plant
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000421 - pollen fertility
 Os04g0498600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g42090.1
LOC_Os04g42090.2
LOC_Os04g42090.3
LOC_Os04g42090.4
LOC_Os04g42090.5
LOC_Os04g42095.1
RF2B RF2b
OsRF2B
OsbZIP30
bZIP30
 bZIP TRANSCRIPTION FACTOR RF2B Transcription factor RF2b
bZIP transcription factor 30
 3 Other
Character as QTL - Yield and productivity
Character as QTL - Plant growth activity
 GO:0045847 - negative regulation of nitrogen utilization
GO:0010167 - response to nitrate
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0042128 - nitrate assimilation
GO:0046983 - protein dimerization activity
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0043565 - sequence-specific DNA binding
 TO:0000397 - grain size
TO:0000357 - growth and development trait
TO:0000396 - grain yield
TO:0000011 - nitrogen sensitivity
TO:0000382 - 1000-seed weight
TO:0000402 - grain width
TO:0000449 - grain yield per plant
TO:0000734 - grain length
TO:0000040 - panicle length
TO:0000207 - plant height
 PO:0009005 - root
PO:0009051 - spikelet
Os03g0336200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g21800.1
LOC_Os03g21800.2
RL9 rl9
SLL1/RL9
SLL1
OsSLL1
OsADD1
ADD1
AH2
OsAH2
CL1
OsCL1
OsKAN1
KAN1
 ROLLED LEAF 9 SHALLOT-LIKE1
SHALLOT-LIKE 1
ROLLED LEAF9
anther dehiscence defected 1
abnormal hull 2
curling leaf 1
KANADI1
OsKANADI1
 9 Coloration - Chlorophyll
Other
Character as QTL - Plant growth activity
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
Reproductive organ - Inflorescence
Vegetative organ - Root
Reproductive organ - Spikelet, flower, glume, awn
Character as QTL - Grain quality
Character as QTL - Yield and productivity
Reproductive organ - panicle
Seed - Morphological traits
Vegetative organ - Culm
 GO:0009685 - gibberellin metabolic process
GO:0045487 - gibberellin catabolic process
GO:0006351 - transcription, DNA-dependent
GO:0009739 - response to gibberellin stimulus
GO:0009957 - epidermal cell fate specification
GO:0051510 - regulation of unidimensional cell growth
GO:0080006 - internode patterning
GO:0048364 - root development
GO:0003677 - DNA binding
GO:0003682 - chromatin binding
GO:0005634 - nucleus
GO:0045892 - negative regulation of transcription, DNA-dependent
GO:0006355 - regulation of transcription, DNA-dependent
GO:0048366 - leaf development
GO:0009555 - pollen development
GO:0010229 - inflorescence development
GO:0012501 - programmed cell death
GO:0042127 - regulation of cell proliferation
GO:0030154 - cell differentiation
GO:0048653 - anther development
GO:0048437 - floral organ development
GO:0001558 - regulation of cell growth
GO:0010088 - phloem development
GO:0010158 - abaxial cell fate specification
GO:0048316 - seed development
 TO:0000085 - leaf rolling
TO:0000397 - grain size
TO:0006022 - floral organ development trait
TO:0000587 - endosperm quality
TO:0000474 - glume opening
TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000207 - plant height
TO:0000421 - pollen fertility
TO:0001006 - adventitious root number
TO:0000165 - panicle exsertion
TO:0000495 - chlorophyll content
TO:0000227 - root length
TO:0002681 - leaf curling
TO:0001012 - lateral root length
TO:0000019 - seedling height
TO:0000657 - spikelet anatomy and morphology trait
TO:0002689 - leaf sheath length
TO:0000072 - awn length
TO:0000166 - gibberellic acid sensitivity
TO:0002675 - gibberellic acid content
TO:0000145 - internode length
TO:0000449 - grain yield per plant
TO:0000653 - seed development trait
TO:0000211 - gel consistency
TO:0000598 - protein content
TO:0000196 - amylose content
TO:0000455 - seed set percent
TO:0000734 - grain length
TO:0000040 - panicle length
TO:0000152 - panicle number
TO:0000382 - 1000-seed weight
TO:0000326 - leaf color
TO:0001027 - net photosynthetic rate
TO:0000135 - leaf length
TO:0000295 - chlorophyll-b content
TO:0002757 - flag leaf length
TO:0000370 - leaf width
TO:0000316 - photosynthetic ability
TO:0000462 - gelatinization temperature
TO:0000656 - root development trait
TO:0000396 - grain yield
TO:0000162 - seed quality
TO:0000053 - pollen sterility
TO:0000391 - seed size
TO:0000655 - leaf development trait
 PO:0001170 - seed development stage
PO:0025034 - leaf
PO:0009051 - spikelet
PO:0009047 - stem
PO:0020104 - leaf sheath
PO:0025426 - phloem development stage
PO:0000017 - vascular leaf primordium
PO:0020148 - shoot apical meristem
PO:0009049 - inflorescence
PO:0001007 - pollen development stage
PO:0009005 - root
PO:0020141 - stem node
PO:0001004 - anther development stage
PO:0025585 - floral organ formation stage
PO:0007520 - root development stage
PO:0020142 - stem internode
PO:0000293 - guard cell
PO:0006019 - leaf abaxial epidermis
PO:0001050 - leaf development stage
Os09g0395300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g23200.1
AGPL2 OsAGPL2
osagpl2
APL2
OsAPL2
AGPiso
sh2
Sh2
GIF2
GAS1
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 2 sativa ADP-glucose pyrophosphorylase large subunit 2
ADP-glucose Pyrophosphorylase large subunit 2
AGPase large subunit 2
AGPase large unit 2
ADP-glucose pyrophosphorylase subunit SH2
GRAIN INCOMPLETE FILLING 2
 1 Seed - Morphological traits - Endosperm
Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Storage substances
 GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0009058 - biosynthetic process
GO:0010035 - response to inorganic substance
GO:0009269 - response to desiccation
GO:0005829 - cytosol
GO:0009536 - plastid
GO:0016779 - nucleotidyltransferase activity
GO:0005978 - glycogen biosynthetic process
GO:0009651 - response to salt stress
GO:0048316 - seed development
GO:0010431 - seed maturation
GO:0010581 - regulation of starch biosynthetic process
GO:0019252 - starch biosynthetic process
 TO:0000162 - seed quality
TO:0000382 - 1000-seed weight
TO:0000394 - drought related trait
TO:0002661 - seed maturation
TO:0000653 - seed development trait
TO:0000480 - nutrient sensitivity
TO:0000104 - floury endosperm
TO:0000696 - starch content
TO:0000100 - shrunken endosperm
TO:0000396 - grain yield
TO:0006001 - salt tolerance
TO:0000590 - grain weight
 PO:0009089 - endosperm
PO:0001170 - seed development stage
PO:0007632 - seed maturation stage
PO:0009010 - seed
PO:0007022 - seed imbibition stage
PO:0009001 - fruit
Os01g0633100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g44220.7
LOC_Os01g44220.6
LOC_Os01g44220.5
LOC_Os01g44220.1
LOC_Os01g44220.2
LOC_Os01g44220.3
LOC_Os01g44220.4
AGPL3 OsAGPL3
APL3
OsAPL3
AGPlar
OsAGPL1
AGPL1
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 3 sativa ADP-glucose pyrophosphorylase large subunit 3
ADP-glucose Pyrophosphorylase large subunit 3
AGPase large subunit 3
AGPase large unit 1
AGPase L1
 5 Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Character as QTL - Yield and productivity
 GO:0009058 - biosynthetic process
GO:0009536 - plastid
GO:0009629 - response to gravity
GO:0009413 - response to flooding
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0016779 - nucleotidyltransferase activity
GO:0019252 - starch biosynthetic process
GO:0009959 - negative gravitropism
 TO:0000207 - plant height
TO:0000567 - tiller angle
TO:0000286 - submergence sensitivity
TO:0000396 - grain yield
TO:0000696 - starch content
TO:0000346 - tiller number
TO:0002693 - gravity response trait
 PO:0009066 - anther
PO:0025034 - leaf
PO:0004006 - mesophyll cell
PO:0005020 - vascular bundle
PO:0020104 - leaf sheath
PO:0000074 - parenchyma cell
PO:0009047 - stem
PO:0009010 - seed
PO:0009089 - endosperm
Os05g0580000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g50380.2
LOC_Os05g50380.1
AGPS2 OsAGPS2a
AGPS2A
AGPS2B
OsAGPS2
osagps2
APS2
APS2a
APS2b
AGPS2a
APGS2b
OsAGPS2b
AGPP
GAS8
OsAPS2
OsAPS2a
OsAPS2b
 ADP-GLUCOSE PYROPHOSPHORYLASE SMALL SUBUNIT 2 sativa ADP-glucose pyrophosphorylase small subunit 2a
sativa ADP-glucose pyrophosphorylase small subunit 2
ADP-glucose Pyrophosphorylase small subunit 2
AGPase small subunit 2
ADP-glucose pyrophosphorylase small subunit 2a
ADP-glucose pyrophosphorylase 51kD subunit
ADP-glucose pyrophosphorylase small unit 2
ADP-glucose pyrophosphorylase small subunit 2b
 8 Seed - Morphological traits - Endosperm
Character as QTL - Yield and productivity
Seed - Physiological traits - Storage substances
Biochemical character
Tolerance and resistance - Stress tolerance
 GO:0009408 - response to heat
GO:0010035 - response to inorganic substance
GO:0009269 - response to desiccation
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0005982 - starch metabolic process
GO:0005829 - cytosol
GO:0019252 - starch biosynthetic process
GO:0005524 - ATP binding
GO:0009501 - amyloplast
GO:0009507 - chloroplast
GO:0009536 - plastid
GO:0009415 - response to water
GO:0000003 - reproduction
GO:0009651 - response to salt stress
GO:0009791 - post-embryonic development
GO:0005978 - glycogen biosynthetic process
 TO:0000394 - drought related trait
TO:0000011 - nitrogen sensitivity
TO:0000480 - nutrient sensitivity
TO:0000237 - water stress trait
TO:0000100 - shrunken endosperm
TO:0000333 - sugar content
TO:0002661 - seed maturation
TO:0000259 - heat tolerance
TO:0000696 - starch content
TO:0000382 - 1000-seed weight
TO:0006001 - salt tolerance
 PO:0025034 - leaf
PO:0007022 - seed imbibition stage
PO:0009010 - seed
PO:0009089 - endosperm
PO:0007632 - seed maturation stage
Os08g0345800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g25734.2
LOC_Os08g25734.1
ABI5 OsABI5
OsbZIP10
OsABF1
OREB1
OsABI5-1
OsABI5-2
OsOREB1
OREB1
 ABA INSENSITIVE 5 ABA Insensitive 5
bZIP-type transcription factor ABI5
bZIP transcription factors OsABI5
bZIP transcription factor 10
Abscisic acid insensitive 5
 1 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
Reproductive organ - Pollination, fertilization, fertility - Male sterility
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
Character as QTL - Germination
Character as QTL - Grain quality
Character as QTL - Yield and productivity
 GO:0009725 - response to hormone stimulus
GO:0010029 - regulation of seed germination
GO:0010162 - seed dormancy
GO:0045449 - regulation of transcription
GO:0009787 - regulation of abscisic acid mediated signaling
GO:0010581 - regulation of starch biosynthetic process
GO:0009737 - response to abscisic acid stimulus
GO:0045454 - cell redox homeostasis
GO:0005982 - starch metabolic process
GO:0006995 - cellular response to nitrogen starvation
GO:0005985 - sucrose metabolic process
GO:0009753 - response to jasmonic acid stimulus
GO:0010187 - negative regulation of seed germination
GO:0042744 - hydrogen peroxide catabolic process
GO:0009409 - response to cold
GO:0046345 - abscisic acid catabolic process
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0051171 - regulation of nitrogen compound metabolic process
GO:0009651 - response to salt stress
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0031667 - response to nutrient levels
GO:0010152 - pollen maturation
GO:0003700 - transcription factor activity
GO:0009845 - seed germination
GO:0042594 - response to starvation
GO:0009739 - response to gibberellin stimulus
GO:0009733 - response to auxin stimulus
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0019740 - nitrogen utilization
GO:0010372 - positive regulation of gibberellin biosynthetic process
GO:0030187 - melatonin biosynthetic process
 TO:0000615 - abscisic acid sensitivity
TO:0000303 - cold tolerance
TO:0000276 - drought tolerance
TO:0000250 - vigor related trait
TO:0000401 - plant growth hormone sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000430 - germination rate
TO:0000696 - starch content
TO:0000196 - amylose content
TO:0000097 - amylopectin content
TO:0000382 - 1000-seed weight
TO:0002658 - starch grain synthesis
TO:0002656 - starch grain shape
TO:0000266 - chalky endosperm
TO:0000399 - grain thickness
TO:0000590 - grain weight
TO:0000134 - alkali digestion
TO:0002667 - abscisic acid content
TO:0000011 - nitrogen sensitivity
TO:0000396 - grain yield
TO:0000172 - jasmonic acid sensitivity
TO:0000053 - pollen sterility
TO:0000253 - seed dormancy
TO:0002672 - auxin content
TO:0000604 - fat and essential oil content
TO:0002653 - endosperm storage protein content
TO:0000300 - glucose content
TO:0000455 - seed set percent
TO:0000040 - panicle length
TO:0000462 - gelatinization temperature
TO:0000211 - gel consistency
TO:0000487 - endosperm color
TO:0000162 - seed quality
TO:0000166 - gibberellic acid sensitivity
TO:0000163 - auxin sensitivity
TO:0000919 - grain weight
TO:0000397 - grain size
TO:0000483 - germinability at low temperature
TO:0000420 - fertility related trait
TO:0000429 - salt sensitivity
 PO:0009049 - inflorescence
PO:0007057 - 0 seed germination stage
PO:0020091 - obsolete microgametophyte
PO:0025500 - whole plant fruit development stage
PO:0009010 - seed
Os01g0859300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g64000.1
LOC_Os01g64000.2
LOC_Os01g64000.3
AGO17 OsAGO17
 ARGONAUTE 17 Protein argonaute 17
 2 Character as QTL - Yield and productivity
Seed - Physiological traits - Storage substances
Other
Seed - Morphological traits
Reproductive organ - panicle
Vegetative organ - Culm
 GO:0003676 - nucleic acid binding
GO:0005739 - mitochondrion
GO:0031047 - gene silencing by RNA
GO:0051512 - positive regulation of unidimensional cell growth
GO:0005634 - nucleus
 TO:0000592 - 1000-dehulled grain weight
TO:0000397 - grain size
TO:0000455 - seed set percent
TO:0000266 - chalky endosperm
TO:0000456 - spikelet number
TO:0000207 - plant height
TO:0000391 - seed size
TO:0000657 - spikelet anatomy and morphology trait
TO:0000590 - grain weight
TO:0000576 - stem length
TO:0000051 - stem strength
TO:0000449 - grain yield per plant
TO:0000734 - grain length
TO:0000040 - panicle length
TO:0000339 - stem thickness
TO:0000145 - internode length
 PO:0020141 - stem node
Os02g0169400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g07310.1
AGO2 OsAGO2
 ARGONAUTE 2 sativa Argonaute 2
Protein argonaute 2
ARGONAUTE2
 4 Tolerance and resistance - Stress tolerance
Other
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Coloration - Chlorophyll
Vegetative organ - Leaf
Seed - Morphological traits - Grain shape
 GO:0009409 - response to cold
GO:0009658 - chloroplast organization
GO:0003676 - nucleic acid binding
GO:0043067 - regulation of programmed cell death
GO:0051607 - defense response to virus
GO:0031047 - gene silencing by RNA
GO:0046466 - membrane lipid catabolic process
GO:0009737 - response to abscisic acid stimulus
GO:0009690 - cytokinin metabolic process
GO:0048316 - seed development
GO:0009651 - response to salt stress
GO:0050687 - negative regulation of defense response to virus
GO:0006306 - DNA methylation
GO:0010150 - leaf senescence
 TO:0000734 - grain length
TO:0000455 - seed set percent
TO:0000615 - abscisic acid sensitivity
TO:0002660 - cytokinin content
TO:0000249 - leaf senescence
TO:0006001 - salt tolerance
TO:0002715 - chloroplast development trait
TO:0000495 - chlorophyll content
TO:0000020 - black streak dwarf virus resistance
TO:0000326 - leaf color
TO:0001015 - photosynthetic rate
TO:0000269 - 100-seed weight
TO:0000605 - hydrogen peroxide content
TO:0000449 - grain yield per plant
TO:0000396 - grain yield
TO:0000316 - photosynthetic ability
TO:0000303 - cold tolerance
 Os04g0615700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g52540.1
BGAL14 OsBgal14
OsBGal14
OsEnS-135
OsMEG2
MEG2
 BETA-GALACTOSIDASE 14 Beta-galactosidase 14
Lactase 14
endosperm-specific gene 135
maternally expressed gene 2
 10 Character as QTL - Yield and productivity
Biochemical character
 GO:0048046 - apoplast
GO:0043169 - cation binding
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0004565 - beta-galactosidase activity
GO:0005975 - carbohydrate metabolic process
GO:0005529 - sugar binding
 TO:0000382 - 1000-seed weight
 Os10g0340600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g19960.1
DCL3B OsDCL3b
 DICER-LIKE 3B Endoribonuclease Dicer homolog 3b
Dicer-like protein 3b
 10 Biochemical character
Seed - Physiological traits - Storage substances
Character as QTL - Yield and productivity
Seed - Physiological traits
 GO:0005634 - nucleus
GO:0008026 - ATP-dependent helicase activity
GO:0009536 - plastid
GO:0030145 - manganese ion binding
GO:0000287 - magnesium ion binding
GO:0003725 - double-stranded RNA binding
GO:0004525 - ribonuclease III activity
GO:0005524 - ATP binding
GO:0006396 - RNA processing
GO:0000380 - alternative nuclear mRNA splicing, via spliceosome
GO:0031047 - gene silencing by RNA
 TO:0000162 - seed quality
TO:0000421 - pollen fertility
TO:0000455 - seed set percent
TO:0002673 - amino acid content
TO:0000396 - grain yield
TO:0000598 - protein content
TO:0000180 - spikelet fertility
 Os10g0485600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g34430.1
LOX1 OsLOX1
OsLOX5
 LIPOXYGENASE 1 lipoxygenase 1
Probable lipoxygenase 4
lipoxygenase 5
 3 Seed - Morphological traits - Embryo
Biochemical character
Seed - Physiological traits
Tolerance and resistance - Stress tolerance
Character as QTL - Grain quality
 GO:0009611 - response to wounding
GO:0009266 - response to temperature stimulus
GO:0009793 - embryonic development ending in seed dormancy
GO:0006521 - regulation of cellular amino acid metabolic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0019216 - regulation of lipid metabolic process
GO:0006629 - lipid metabolic process
GO:0005506 - iron ion binding
GO:0016165 - lipoxygenase activity
GO:0031408 - oxylipin biosynthetic process
GO:0055114 - oxidation reduction
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0006979 - response to oxidative stress
 TO:0000196 - amylose content
TO:0006001 - salt tolerance
TO:0005001 - linoleic acid content
TO:0000435 - seed longevity
TO:0002657 - oxidative stress
TO:0000432 - temperature response trait
TO:0000620 - embryo development trait
TO:0000276 - drought tolerance
TO:0000345 - seed viability
TO:0000696 - starch content
TO:0000162 - seed quality
TO:0000211 - gel consistency
 PO:0007631 - plant embryo stage
Os03g0700700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g49380.3
LOC_Os03g49380.2
LOC_Os03g49380.1
HLM1 NRAMP4
OsNRAMP4
Nrat1
Nramp6
OsNRAT1
NRAT1
FCO5
 HR-LIKE LESION MIMIC 1 BACTERIOCIDE EFFECT 4
Nramp aluminum transporter 1
Functioning in Cesium Over-transport 5
HR-like lesion mimic 1
 2 Tolerance and resistance - Lesion mimic
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Plant growth activity
Tolerance and resistance - Disease resistance
 GO:0043068 - positive regulation of programmed cell death
GO:0015083 - aluminum ion transmembrane transporter activity
GO:0043410 - positive regulation of MAPKKK cascade
GO:0016021 - integral to membrane
GO:0005737 - cytoplasm
GO:0042742 - defense response to bacterium
GO:0052322 - positive regulation of phytoalexin biosynthetic process
GO:0005886 - plasma membrane
GO:0010044 - response to aluminum ion
GO:0030001 - metal ion transport
 TO:0000516 - relative root length
TO:0000063 - mimic response
TO:0000175 - bacterial blight disease resistance
TO:0000605 - hydrogen peroxide content
TO:0000357 - growth and development trait
TO:0000207 - plant height
TO:0002757 - flag leaf length
TO:0002758 - flag leaf lamina width
TO:0000040 - panicle length
TO:0000734 - grain length
TO:0000354 - aluminum sensitivity
TO:0000455 - seed set percent
TO:0000447 - filled grain number
TO:0000382 - 1000-seed weight
 PO:0025034 - leaf
Os02g0131800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g03900.1
CKX1 OsCKX1
 CYTOKININ OXIDASE/DEHYDROGENASE 1 cytokinin oxidase 1
 1 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Biochemical character
Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
 GO:0042594 - response to starvation
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0009725 - response to hormone stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0009823 - cytokinin catabolic process
GO:0009793 - embryonic development ending in seed dormancy
GO:0019139 - cytokinin dehydrogenase activity
 TO:0000167 - cytokinin sensitivity
TO:0000011 - nitrogen sensitivity
TO:0002660 - cytokinin content
TO:0000163 - auxin sensitivity
TO:0000401 - plant growth hormone sensitivity
TO:0000620 - embryo development trait
TO:0000266 - chalky endosperm
 PO:0007631 - plant embryo stage
PO:0009005 - root
Os01g0187600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g09260.1
CKX3 OsCKX3
ckx3
 CYTOKININ OXIDASE/DEHYDROGENASE 3 Putative cytokinin oxidase 3
cytokinin oxidase 3
 10 Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Biochemical character
 GO:0032940 - secretion by cell
GO:0050660 - FAD binding
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0005615 - extracellular space
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0016491 - oxidoreductase activity
GO:0019139 - cytokinin dehydrogenase activity
GO:0022900 - electron transport chain
GO:0009735 - response to cytokinin stimulus
 TO:0000266 - chalky endosperm
TO:0000167 - cytokinin sensitivity
 PO:0009005 - root
Os10g0483500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g34230.1
CKX4 OsCKX4
ckx4
OsSCRM
OsSCRM2
SCRM
SCRM2
 CYTOKININ OXIDASE/DEHYDROGENASE 4 Putative cytokinin dehydrogenase 4
cytokinin oxidase 4
 1 Character as QTL - Grain quality
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
Biochemical character
 GO:0009725 - response to hormone stimulus
GO:0019139 - cytokinin dehydrogenase activity
GO:0048364 - root development
GO:0009736 - cytokinin mediated signaling
GO:0042594 - response to starvation
GO:0009735 - response to cytokinin stimulus
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0032940 - secretion by cell
GO:0009733 - response to auxin stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009734 - auxin mediated signaling pathway
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0022900 - electron transport chain
GO:0016491 - oxidoreductase activity
GO:0051607 - defense response to virus
GO:0009823 - cytokinin catabolic process
 TO:0000227 - root length
TO:0000346 - tiller number
TO:0000456 - spikelet number
TO:0000401 - plant growth hormone sensitivity
TO:0006032 - panicle size
TO:0000734 - grain length
TO:0000402 - grain width
TO:0002660 - cytokinin content
TO:0000656 - root development trait
TO:0000011 - nitrogen sensitivity
TO:0000207 - plant height
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000148 - viral disease resistance
TO:0000019 - seedling height
TO:0000020 - black streak dwarf virus resistance
TO:0000382 - 1000-seed weight
TO:0000172 - jasmonic acid sensitivity
TO:0002685 - crown root number
TO:0000449 - grain yield per plant
TO:0000430 - germination rate
TO:0000455 - seed set percent
 PO:0009105 - inflorescence branch meristem
PO:0009005 - root
PO:0007520 - root development stage
PO:0025034 - leaf
Os01g0940000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g71310.1
CKX5 OsCKX5
ckx5
 CYTOKININ OXIDASE/DEHYDROGENASE 5 Putative cytokinin oxidase 5
cytokinin oxidase 5
 1 Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Biochemical character
Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
 GO:0042594 - response to starvation
GO:0032940 - secretion by cell
GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009694 - jasmonic acid metabolic process
GO:0009753 - response to jasmonic acid stimulus
GO:0009725 - response to hormone stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0009823 - cytokinin catabolic process
GO:0009536 - plastid
GO:0016491 - oxidoreductase activity
GO:0019139 - cytokinin dehydrogenase activity
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0050660 - FAD binding
GO:0022900 - electron transport chain
 TO:0002660 - cytokinin content
TO:0000207 - plant height
TO:0000401 - plant growth hormone sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000266 - chalky endosperm
TO:0000011 - nitrogen sensitivity
TO:0000163 - auxin sensitivity
 Os01g0775400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g56810.2
LOC_Os01g56810.1
CKX6 OsCKX6
 CYTOKININ OXIDASE/DEHYDROGENASE 6 cytokinin oxidase 6
 2 Reproductive organ - panicle
Seed - Physiological traits - Storage substances
Character as QTL - Yield and productivity
Character as QTL - Grain quality
Biochemical character
 GO:0005615 - extracellular space
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0019139 - cytokinin dehydrogenase activity
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
 TO:0002660 - cytokinin content
TO:0002759 - grain number
TO:0000040 - panicle length
TO:0000266 - chalky endosperm
 Os02g0220000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 )
CKX7 OsCKX7
 CYTOKININ OXIDASE/DEHYDROGENASE 7 cytokinin oxidase 7
 2 Biochemical character
Reproductive organ - panicle
Seed - Physiological traits - Storage substances
Character as QTL - Grain quality
Seed - Morphological traits - Grain shape
Tolerance and resistance - Disease resistance
Character as QTL - Yield and productivity
 GO:0019139 - cytokinin dehydrogenase activity
GO:0050660 - FAD binding
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0005615 - extracellular space
GO:0050832 - defense response to fungus
GO:0009823 - cytokinin catabolic process
 TO:0000734 - grain length
TO:0000255 - sheath blight disease resistance
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000402 - grain width
TO:0000266 - chalky endosperm
TO:0000455 - seed set percent
 PO:0020104 - leaf sheath
Os02g0220100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g12780.1
CKX9 OsCKX9
 CYTOKININ OXIDASE/DEHYDROGENASE 9 cytokinin oxidase 9
 5 Biochemical character
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Character as QTL - Yield and productivity
 GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009690 - cytokinin metabolic process
GO:0050660 - FAD binding
GO:0009735 - response to cytokinin stimulus
GO:0009733 - response to auxin stimulus
GO:0009725 - response to hormone stimulus
GO:0042594 - response to starvation
GO:0005829 - cytosol
GO:0009823 - cytokinin catabolic process
GO:0005634 - nucleus
GO:0019139 - cytokinin dehydrogenase activity
 TO:0000547 - primary branch number
TO:0000011 - nitrogen sensitivity
TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000207 - plant height
TO:0000401 - plant growth hormone sensitivity
TO:0000582 - inflorescence number
TO:0000040 - panicle length
TO:0002660 - cytokinin content
TO:0000447 - filled grain number
TO:0000346 - tiller number
 Os05g0374200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g31040.1
CKX10 OsCKX10
 CYTOKININ OXIDASE/DEHYDROGENASE 10 cytokinin oxidase 10
 6 Character as QTL - Grain quality
Biochemical character
Seed - Physiological traits - Storage substances
 GO:0005615 - extracellular space
GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0050660 - FAD binding
GO:0019139 - cytokinin dehydrogenase activity
GO:0009690 - cytokinin metabolic process
 TO:0000266 - chalky endosperm
 Os06g0572300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g37500.1
CKX11 OsCKX11
 CYTOKININ OXIDASE/DEHYDROGENASE 11 cytokinin oxidase 11
 8 Character as QTL - Yield and productivity
Biochemical character
Character as QTL - Grain quality
Seed - Physiological traits - Storage substances
Reproductive organ - Panicle, Mode of branching
 GO:0008762 - UDP-N-acetylmuramate dehydrogenase activity
GO:0009735 - response to cytokinin stimulus
GO:0019139 - cytokinin dehydrogenase activity
GO:0005615 - extracellular space
GO:0050660 - FAD binding
GO:0009690 - cytokinin metabolic process
 TO:0000167 - cytokinin sensitivity
TO:0002660 - cytokinin content
TO:0000266 - chalky endosperm
TO:0000455 - seed set percent
TO:0000557 - secondary branch number
TO:0000547 - primary branch number
TO:0002759 - grain number
 Os08g0460600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g35860.1
GT1 HOX12
Oshox12
OsHox12
OsGT1
 GRASSY TILLER 1 rice homeobox gene 12
Homeobox-leucine zipper protein HOX12
Homeodomain transcription factor HOX12
HD-ZIP protein HOX12
grassy tiller1
 3 Reproductive organ - panicle
Tolerance and resistance - Stress tolerance
Character as QTL - Germination
Other
Vegetative organ - Culm
 GO:0003700 - transcription factor activity
GO:0009845 - seed germination
GO:0005634 - nucleus
GO:0009413 - response to flooding
GO:0009409 - response to cold
GO:0009685 - gibberellin metabolic process
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0030912 - response to deep water
GO:0043565 - sequence-specific DNA binding
GO:0048658 - tapetal layer development
GO:0010336 - gibberellic acid homeostasis
 TO:0000329 - tillering ability
TO:0000346 - tiller number
TO:0002675 - gibberellic acid content
TO:0001002 - inflorescence exsertion
TO:0000303 - cold tolerance
TO:0000524 - submergence tolerance
 PO:0007045 - coleoptile emergence stage
PO:0009049 - inflorescence
PO:0009066 - anther
PO:0007057 - 0 seed germination stage
Os03g0198600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g10210.1
HOX29 Oshox29
OsHox29
OSHB5
HB5
 HOMEOBOX GENE 29 rice homeobox gene 29
Homeobox-leucine zipper protein HOX29
Homeodomain transcription factor HOX29
HD-ZIP protein HOX29
HOMEODOMAIN CONTAINING PROTEIN 5
 1 Other
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
 GO:0003700 - transcription factor activity
GO:0006350 - transcription
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0006355 - regulation of transcription, DNA-dependent
 TO:0000397 - grain size
 Os01g0200300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g10320.1
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