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Search Condition : Filter((traitClassFacetEn:030_Seed - Physiological traits OR traitClassFacetEn:031_Seed - Physiological traits - Dormancy OR traitClassFacetEn:032_Seed - Physiological traits - Longevity OR traitClassFacetEn:033_Seed - Physiological traits - Storage substances OR traitClassFacetEn:034_Seed - Physiological traits - Shattering OR traitClassFacetEn:035_Seed - Physiological traits - Taste))
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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
GID1 gid1
OsGID1
Thl
Os GID1
 GIBBERELLIN INSENSITIVE DWARF1 GIBBERELLIN-INSENSITIVE DWARF1
Gibberellin receptor GID1
Gibberellin-insensitive dwarf protein 1
Protein GIBBERELLIN INSENSITIVE DWARF1
Thumbelina
GA-insensitive dwarf 1
 5 Vegetative organ - Culm
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Dormancy
 GO:0004872 - receptor activity
GO:0010162 - seed dormancy
GO:0010271 - regulation of chlorophyll catabolic process
GO:0009414 - response to water deprivation
GO:0009738 - abscisic acid mediated signaling
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0006109 - regulation of carbohydrate metabolic process
GO:0009740 - gibberellic acid mediated signaling
GO:0009737 - response to abscisic acid stimulus
GO:0014001 - sclerenchyma cell differentiation
GO:2000037 - regulation of stomatal complex patterning
GO:2000038 - regulation of stomatal complex development
GO:0008152 - metabolic process
GO:0005634 - nucleus
GO:0016787 - hydrolase activity
GO:0009409 - response to cold
GO:0050832 - defense response to fungus
GO:0009739 - response to gibberellin stimulus
GO:0009609 - response to symbiotic bacterium
 TO:0000566 - stomatal frequency
TO:0000286 - submergence sensitivity
TO:0000495 - chlorophyll content
TO:0000074 - blast disease
TO:0000135 - leaf length
TO:0000175 - bacterial blight disease resistance
TO:0000207 - plant height
TO:0000276 - drought tolerance
TO:0000615 - abscisic acid sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000303 - cold tolerance
TO:0000253 - seed dormancy
TO:0000291 - carbohydrate content
TO:0000470 - vascular tissue related trait
 Os05g0407500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g33730.1
NPP1 OsNPP1
OsPAP27b
PAP27B
 NUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 1 Nucleotide Pyrophosphatase/Phosphodiesterase 1
Purple acid phosphatase 27b
 8 Tolerance and resistance - Stress tolerance
Biochemical character
Seed - Physiological traits - Storage substances
 GO:0001666 - response to hypoxia
GO:0004528 - phosphodiesterase I activity
GO:0046872 - metal ion binding
GO:0003993 - acid phosphatase activity
GO:0004551 - nucleotide diphosphatase activity
GO:0005618 - cell wall
 TO:0000233 - root volume
TO:0000207 - plant height
TO:0000015 - oxygen sensitivity
TO:0000696 - starch content
 Os08g0531000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g41880.1
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
RPBF OsDof3
OsDOF3
OsEnS-34
OsDof10
Dof10
OsDof-10
OsDOF1
DOF1
DOF3
OsRPBF
OsDOF7
 RICE PROLAMIN BOX BINDING FACTOR rice (Oryza sativa) prolamin box binding factor
pyrimidine box-binding protein
endosperm-specific gene 34
Dof zinc factor 10
Dof transcription factor 10
DNA BINDING WITH ONE FINGER 10
 2 Seed - Physiological traits - Storage substances
Tolerance and resistance
Tolerance and resistance - Stress tolerance
Other
Seed - Physiological traits - Longevity
Seed - Physiological traits
 GO:0006952 - defense response
GO:0009651 - response to salt stress
GO:0008270 - zinc ion binding
GO:0009414 - response to water deprivation
GO:0010029 - regulation of seed germination
GO:0003677 - DNA binding
GO:0006979 - response to oxidative stress
GO:0006970 - response to osmotic stress
GO:0045449 - regulation of transcription
 TO:0000179 - biotic stress trait
TO:0006004 - raffinose content
TO:0002673 - amino acid content
TO:0000250 - vigor related trait
TO:0000276 - drought tolerance
TO:0000430 - germination rate
TO:0006001 - salt tolerance
TO:0002657 - oxidative stress
TO:0000095 - osmotic response sensitivity
 PO:0009010 - seed
PO:0001170 - seed development stage
Os02g0252400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g15350.1
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
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
SSIIB OsSSIIb
OsSSII-2
SSII-2
SS2
OsSSSIIb
SS2b
 SOLUBLE STARCH SYNTHASE IIB Starch synthase-IIb
starch synthase IIb
"Soluble starch synthase 2-2
chloroplastic/amyloplastic"
Soluble starch synthase II-2
Starch synthase isoform zSTSII-2
 2 Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
 GO:0019252 - starch biosynthetic process
GO:0009651 - response to salt stress
GO:0009507 - chloroplast
GO:0009501 - amyloplast
GO:0009011 - starch synthase activity
 TO:0000488 - seed composition based quality trait
TO:0006001 - salt tolerance
 PO:0025034 - leaf
PO:0009009 - plant embryo
PO:0009072 - plant ovary
PO:0009010 - seed
Os02g0744700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g51070.1
SSIIC OsSSIIc
SSII-1
SSII1
 SOLUBLE STARCH SYNTHASE IIC "Soluble starch synthase 2-1
chloroplastic/amyloplastic"
Soluble starch synthase II-1
 10 Seed - Physiological traits - Storage substances
 GO:0009507 - chloroplast
GO:0009501 - amyloplast
GO:0019252 - starch biosynthetic process
GO:0009011 - starch synthase activity
GO:0009733 - response to auxin stimulus
GO:0080026 - response to indolebutyric acid stimulus
 TO:0000163 - auxin sensitivity
 PO:0009089 - endosperm
PO:0025034 - leaf
Os10g0437600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g30156.1
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
SSIVA OsSSIVa
SSIV-1
OsSSIV-1
 SOLUBLE STARCH SYNTHASE IVA SOLUBLE STARCH SYNTHASE IV-1
 1 Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
 GO:0009501 - amyloplast
GO:0009507 - chloroplast
GO:0009269 - response to desiccation
GO:0019252 - starch biosynthetic process
GO:0009651 - response to salt stress
GO:0009250 - glucan biosynthetic process
GO:0010229 - inflorescence development
GO:0009011 - starch synthase activity
 TO:0000394 - drought related trait
TO:0000621 - inflorescence development trait
TO:0006001 - salt tolerance
 PO:0025034 - leaf
PO:0009089 - endosperm
PO:0001083 - inflorescence development stage
PO:0009072 - plant ovary
PO:0009009 - plant embryo
Os01g0720600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g52250.6
LOC_Os01g52250.5
LOC_Os01g52250.4
LOC_Os01g52250.3
LOC_Os01g52250.1
LOC_Os01g52250.2
SSIVB OsSSIVb
SSIV-2
OsSSIV-2
SSIVb
SSIV-2
SSIV2
OsSSIV2
 SOLUBLE STARCH SYNTHASE IVB SOLUBLE STARCH SYNTHASE IV-2
 5 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
 GO:0009269 - response to desiccation
GO:0009011 - starch synthase activity
GO:0009507 - chloroplast
GO:0005978 - glycogen biosynthetic process
GO:0009960 - endosperm development
GO:0009501 - amyloplast
GO:0019252 - starch biosynthetic process
 TO:0000394 - drought related trait
 PO:0025034 - leaf
PO:0009089 - endosperm
PO:0007633 - endosperm development stage
Os05g0533600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g45720.4
LOC_Os05g45720.3
LOC_Os05g45720.2
LOC_Os05g45720.1
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
SBE4 RBE4
OsSBE4
BEIIa
QEIIb
BEIIA
OsBEIIa
 STARCH BRANCHING ENZYME 4 Q-enzyme IIb
starch branching enzyme IIb
Starch branching enzyme IIa
 4 Seed - Physiological traits - Storage substances
Seed - Morphological traits - Grain shape
 GO:0005982 - starch metabolic process
GO:0019252 - starch biosynthetic process
GO:0003844 - 1,4-alpha-glucan branching enzyme activity
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0005976 - polysaccharide metabolic process
GO:0009501 - amyloplast
GO:0009568 - amyloplast starch grain
 TO:0000099 - sugary endosperm
TO:0000097 - amylopectin content
TO:0000162 - seed quality
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0000489 - carbohydrate composition related trait
 PO:0025034 - leaf
Os04g0409200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g33460.1
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
YUCCA9 OsYUCCA9
OsYUC9
YUC9
 YUCCA-LIKE GENE 9 (YUCCA-like gene)
 1 Seed - Morphological traits - Embryo
Seed - Morphological traits - Endosperm
Seed - Physiological traits - Storage substances
Biochemical character
 GO:0048316 - seed development
GO:0010262 - somatic embryogenesis
GO:0009851 - auxin biosynthetic process
GO:0004499 - flavin-containing monooxygenase activity
 TO:0002672 - auxin content
TO:0000653 - seed development trait
TO:0000266 - chalky endosperm
 PO:0009089 - endosperm
PO:0000423 - plant zygote
PO:0009006 - shoot system
PO:0009005 - root
PO:0009009 - plant embryo
PO:0009047 - stem
PO:0001170 - seed development stage
PO:0009049 - inflorescence
Os01g0273800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g16714.1
BAD1 Badh1
badh1
BAD1
BADH1
OsBADH1
BADH
OsALDH10A5
ALDH10A5
 BETAINE ALDEHYDE DEHYDROGENASE 1 betaine aldehyde dehydrogenase 1
Aldehyde dehydrogenase 10A5
 4 Biochemical character
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Taste
 GO:0009409 - response to cold
GO:0009651 - response to salt stress
GO:0010728 - regulation of hydrogen peroxide biosynthetic process
GO:0009408 - response to heat
GO:0009416 - response to light stimulus
GO:0008802 - betaine-aldehyde dehydrogenase activity
GO:0009414 - response to water deprivation
GO:0010037 - response to carbon dioxide
GO:0005618 - cell wall
GO:0005777 - peroxisome
GO:0019285 - glycine betaine biosynthetic process from choline
GO:0009413 - response to flooding
 TO:0000075 - light sensitivity
TO:0000303 - cold tolerance
TO:0000276 - drought tolerance
TO:0000087 - aroma
TO:0000286 - submergence sensitivity
TO:0000259 - heat tolerance
TO:0006001 - salt tolerance
 Os04g0464200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g39020.1
PT4 OsPT4
PHT1-4
OsPht1;4
PHT1-2
PHT1;4
OsPHT1;4
 PHOSPHATE TRANSPORTER 4 Probable inorganic phosphate transporter 1-4
Plant Phosphate Transporter 1;4
 4 Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
Seed - Physiological traits - Dormancy
Biochemical character
 GO:0001887 - selenium metabolic process
GO:0009609 - response to symbiotic bacterium
GO:0046685 - response to arsenic
GO:0005315 - inorganic phosphate transmembrane transporter activity
GO:0005886 - plasma membrane
GO:0009790 - embryonic development
GO:0006817 - phosphate transport
GO:0009845 - seed germination
GO:0015293 - symporter activity
GO:0009737 - response to abscisic acid stimulus
GO:0009733 - response to auxin stimulus
GO:0009735 - response to cytokinin stimulus
GO:0016020 - membrane
GO:0009739 - response to gibberellin stimulus
GO:0016021 - integral to membrane
GO:0046688 - response to copper ion
GO:0042594 - response to starvation
GO:0055085 - transmembrane transport
GO:0016036 - cellular response to phosphate starvation
GO:0010269 - response to selenium ion
 TO:0000163 - auxin sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000166 - gibberellic acid sensitivity
TO:0000615 - abscisic acid sensitivity
TO:0000021 - copper sensitivity
TO:0000102 - phosphorus sensitivity
 PO:0007633 - endosperm development stage
PO:0009009 - plant embryo
PO:0007057 - 0 seed germination stage
PO:0020103 - flag leaf
PO:0001170 - seed development stage
PO:0007631 - plant embryo stage
PO:0007632 - seed maturation stage
Os04g0186400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os04g10750.4
LOC_Os04g10750.1
LOC_Os04g10750.2
LOC_Os04g10750.3
GER5 OsGLP1
GLP1
GER1
GLP110
OsGER1
OsGER5
OsGLP8-14
GLP8-14
OsCDP8.14
CDP8.14
 GERMIN-LIKE PROTEIN 5 Germin-like protein 8-14
Germin-like protein 5
Germin-like protein 1
Germin protein type 1
germin-like protein1
cupin domain protein 8.14
 8 Reproductive organ - panicle
Vegetative organ - Leaf
Vegetative organ - Root
Tolerance and resistance - Stress tolerance
Vegetative organ - Culm
Tolerance and resistance - Disease resistance
Seed - Physiological traits - Storage substances
 GO:0005829 - cytosol
GO:0010109 - regulation of photosynthesis
GO:0051553 - flavone biosynthetic process
GO:0010941 - regulation of cell death
GO:0051555 - flavonol biosynthetic process
GO:0010229 - inflorescence development
GO:0009812 - flavonoid metabolic process
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0010224 - response to UV-B
GO:0009409 - response to cold
 TO:0000227 - root length
TO:0001027 - net photosynthetic rate
TO:0000605 - hydrogen peroxide content
TO:0000601 - UV-B light sensitivity
TO:0000207 - plant height
TO:0000621 - inflorescence development trait
TO:0000303 - cold tolerance
TO:0000206 - leaf angle
TO:0000063 - mimic response
 PO:0001083 - inflorescence development stage
PO:0020104 - leaf sheath
Os08g0460000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g35760.1
GLP12-1 OsGLP12-1
OsCDP12.1
CDP12.1
 GERMIN-LIKE PROTEIN 12-1 Germin-like protein 12-1
cupin domain protein 12.1
 12 Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
 GO:0048046 - apoplast
GO:0050832 - defense response to fungus
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
 TO:0000074 - blast disease
 Os12g0154700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g05840.1
GLP12-2 OsGLP12-2
OsCDP12.2
CDP12.2
 GERMIN-LIKE PROTEIN 12-2 Germin-like protein 12-2
cupin domain protein 12.2
 12 Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
 GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0050832 - defense response to fungus
 TO:0000477 - panicle blast disease resistance
 Os12g0154800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g05860.1
GLP12-3 OsGLP12-3
OsCDP12.3
CDP12.3
 GERMIN-LIKE PROTEIN 12-3 cupin domain protein 12.3
 12 Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
 GO:0046686 - response to cadmium ion
GO:0009414 - response to water deprivation
GO:0009737 - response to abscisic acid stimulus
GO:0009413 - response to flooding
GO:0009753 - response to jasmonic acid stimulus
GO:0006970 - response to osmotic stress
GO:0009651 - response to salt stress
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0030145 - manganese ion binding
GO:0009269 - response to desiccation
GO:0016023 - cytoplasmic membrane-bounded vesicle
 TO:0000172 - jasmonic acid sensitivity
TO:0000095 - osmotic response sensitivity
TO:0000114 - flooding related trait
TO:0000276 - drought tolerance
TO:0006001 - salt tolerance
TO:0000615 - abscisic acid sensitivity
 Os12g0154900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os12g05870.1
GLP8-11 OsGLP8-11
RGLP1
OsRGLP1
OsCDP8.11
CDP8.11
 GERMIN-LIKE PROTEIN 8-11 Germin-like protein 8-11
cupin domain protein 8.11
 8 Tolerance and resistance - Disease resistance
Seed - Physiological traits - Storage substances
Tolerance and resistance
Tolerance and resistance - Stress tolerance
 GO:0009414 - response to water deprivation
GO:0046688 - response to copper ion
GO:0046686 - response to cadmium ion
GO:0002242 - defense response to parasitic plant
GO:0009651 - response to salt stress
GO:0005618 - cell wall
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0050832 - defense response to fungus
GO:0009723 - response to ethylene stimulus
GO:0030912 - response to deep water
 TO:0006001 - salt tolerance
TO:0000444 - parasitic weed
TO:0000173 - ethylene sensitivity
TO:0000074 - blast disease
TO:0000286 - submergence sensitivity
TO:0000021 - copper sensitivity
TO:0000276 - drought tolerance
 PO:0009010 - seed
Os08g0190100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g09080.2
LOC_Os08g09080.1
GLP8-12 OsGLP8-12
OsCDP8.12
CDP8.12
 GERMIN-LIKE PROTEIN 8-12 Germin-like protein 8-12
cupin domain protein 8.12
 8 Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0009409 - response to cold
GO:0050832 - defense response to fungus
GO:0048046 - apoplast
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0009723 - response to ethylene stimulus
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
 TO:0000074 - blast disease
TO:0000303 - cold tolerance
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000173 - ethylene sensitivity
 Os08g0231400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g13440.3
LOC_Os08g13440.2
LOC_Os08g13440.1
GER3 OsGLP8-2
GLP8-2
OsGER3
GLP16
OsEnS-117
OsCDP8.2
CDP8.2
 GERMIN-LIKE PROTEIN 3 Germin-like protein 8-2
Germin-like protein 3
Germin-like protein 16
endosperm-specific gene 117
cupin domain protein 8.2
 8 Seed
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
 GO:0006979 - response to oxidative stress
GO:0048316 - seed development
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0046688 - response to copper ion
GO:0046686 - response to cadmium ion
 TO:0000731 - lignin content
TO:0001016 - relative chlorophyll content
TO:0000143 - relative biomass
TO:0000516 - relative root length
TO:0001034 - relative plant height
TO:0000021 - copper sensitivity
TO:0000653 - seed development trait
TO:0000605 - hydrogen peroxide content
TO:0002657 - oxidative stress
 PO:0009010 - seed
PO:0001170 - seed development stage
Os08g0189100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g08960.1
GLP8-5 OsGLP8-5
OsCDP8.5
CDP8.5
 GERMIN-LIKE PROTEIN 8-5 Germin-like protein 8-5
cupin domain protein 8.5
 8 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
 GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0046686 - response to cadmium ion
GO:0046688 - response to copper ion
 TO:0000021 - copper sensitivity
 Os08g0189400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g08990.1
GLP8-6 OsGLP8-6
OsCDP8.6
CDP8.6
 GERMIN-LIKE PROTEIN 8-6 Germin-like protein 8-6
cupin domain protein 8.6
 8 Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
 GO:0046688 - response to copper ion
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
 TO:0000021 - copper sensitivity
 Os08g0189500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g09000.1
GER6 OsGLP8-7
GLP8-7
OsGER6
OsRGLP2
RGLP2
OsCDP8.7
CDP8.7
 GERMIN-LIKE PROTEIN 6 Germin-like protein 8-7
Germin-like protein 6
germin-like protein gene 2
Root GLP 2
root GLP2
root Germin-like protein 2
cupin domain protein 8.7
 8 Seed - Physiological traits - Storage substances
Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Tolerance and resistance
 GO:0009414 - response to water deprivation
GO:0009611 - response to wounding
GO:0009651 - response to salt stress
GO:0010729 - positive regulation of hydrogen peroxide biosynthetic process
GO:0050832 - defense response to fungus
GO:0002213 - defense response to insect
GO:0005618 - cell wall
GO:0046686 - response to cadmium ion
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
GO:0009409 - response to cold
GO:0034059 - response to anoxia
GO:0042742 - defense response to bacterium
GO:0046688 - response to copper ion
GO:0002242 - defense response to parasitic plant
 TO:0000021 - copper sensitivity
TO:0000401 - plant growth hormone sensitivity
TO:0000605 - hydrogen peroxide content
TO:0000249 - leaf senescence
TO:0000188 - drought sensitivity
TO:0000112 - disease resistance
TO:0000303 - cold tolerance
TO:0000424 - brown planthopper resistance
TO:0000315 - bacterial disease resistance
TO:0000439 - fungal disease resistance
TO:0000075 - light sensitivity
TO:0000167 - cytokinin sensitivity
TO:0006001 - salt tolerance
TO:0000168 - abiotic stress trait
TO:0000015 - oxygen sensitivity
TO:0000074 - blast disease
TO:0000444 - parasitic weed
 PO:0009010 - seed
Os08g0189600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g09010.1
GLP8-8 OsGLP8-8
OsCDP8.8
CDP8.8
 GERMIN-LIKE PROTEIN 8-8 Germin-like protein 8-8
cupin domain protein 8.8
 8 Tolerance and resistance - Disease resistance
Seed - Physiological traits - Storage substances
 GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
 Os08g0189700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g09020.1
GLP8-9 OsGLP8-9
OsCDP8.9
CDP8.9
 GERMIN-LIKE PROTEIN 8-9 Germin-like protein 8-9
cupin domain protein 8.9
 8 Seed - Physiological traits - Storage substances
Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
 GO:0046688 - response to copper ion
GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0030145 - manganese ion binding
GO:0045735 - nutrient reservoir activity
GO:0048046 - apoplast
 TO:0000021 - copper sensitivity
 Os08g0189850 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os08g09040.1
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
AGPL4 OsAGPL4
APL4
OsAPL4
OsSTA193
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 4 sativa ADP-glucose pyrophosphorylase large subunit 4
ADP-glucose Pyrophosphorylase large subunit 4
AGPase large subunit 4
AGPase large unit 4
 7 Seed - Morphological traits - Endosperm
Seed - Physiological traits - Storage substances
Reproductive organ - Spikelet, flower, glume, awn
Biochemical character
 GO:0016779 - nucleotidyltransferase activity
GO:0019252 - starch biosynthetic process
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
GO:0009058 - biosynthetic process
GO:0009536 - plastid
 TO:0000106 - male sterility type
TO:0000696 - starch content
 PO:0009066 - anther
PO:0009089 - endosperm
Os07g0243200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g13980.1
AGPS1 OsAGPS1
APS1
OsAPS1
AGPsma
 ADP-GLUCOSE PYROPHOSPHORYLASE SMALL SUBUNIT 1 ADP-glucose pyrophosphorylase small subunit 1
ADP-glucose Pyrophosphorylase small subunit 1
AGPase small subunit 1
Adenosine diphosphate glucose pyrophosphorylase
adenosine diphosphoglucose pyrophosphorylase
ADP-glucose pyrophosphorylase small unit 1
AGPase S1
glucose-1-phosphate adenylyl transferase large subunit
ADP-Glc pyrophosphorylase small subunit 1
AGPase small subunit 1
 9 Tolerance and resistance - Disease resistance
Seed - Physiological traits - Taste
Tolerance and resistance - Stress tolerance
Biochemical character
 GO:0009408 - response to heat
GO:0009413 - response to flooding
GO:0009501 - amyloplast
GO:0009536 - plastid
GO:0009058 - biosynthetic process
GO:0019252 - starch biosynthetic process
GO:0016779 - nucleotidyltransferase activity
GO:0042742 - defense response to bacterium
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
 TO:0000203 - bacterial leaf streak disease resistance
TO:0000266 - chalky endosperm
TO:0000259 - heat tolerance
TO:0000286 - submergence sensitivity
 PO:0020104 - leaf sheath
PO:0009089 - endosperm
PO:0007632 - seed maturation stage
PO:0009047 - stem
PO:0009066 - anther
PO:0004006 - mesophyll cell
PO:0025034 - leaf
PO:0009010 - seed
Os09g0298200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g12660.1
LOC_Os09g12660.2
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
AGO1C OsAGO1c
OsAGO1
AGO1
AGO1c
 ARGONAUTE 1C Protein argonaute 1C
Protein argonaute 1
argonaute1
 2 Seed - Physiological traits
Other
 GO:0031047 - gene silencing by RNA
GO:0003676 - nucleic acid binding
 TO:0000345 - seed viability
 Os02g0831600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g58490.1
AGPL1 OsAGPL1
OsAPL1
APL1
OsAGPL3
AGPL3
OsAGPSL3
AGPSL3
 ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1 sativa ADP-glucose pyrophosphorylase large subunit 1
ADP-glucose Pyrophosphorylase large subunit 1
AGPase large subunit 1
ADP-glucose pyrophosphorylase large subunit 3
AGPase large unit 3
 3 Tolerance and resistance - Stress tolerance
Seed - Physiological traits - Storage substances
Biochemical character
Vegetative organ - Culm
Seed - Morphological traits - Endosperm
 GO:0009629 - response to gravity
GO:0005978 - glycogen biosynthetic process
GO:0009058 - biosynthetic process
GO:0019252 - starch biosynthetic process
GO:0016779 - nucleotidyltransferase activity
GO:0009959 - negative gravitropism
GO:0009536 - plastid
GO:0008878 - glucose-1-phosphate adenylyltransferase activity
 TO:0000696 - starch content
TO:0002693 - gravity response trait
TO:0000567 - tiller angle
 PO:0025034 - leaf
Os03g0735000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g52460.1
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
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
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
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
REG2 REG-2
 RICE EMBRYO GLOBULIN-2 PROTEIN Seed - Morphological traits - Embryo
Seed - Physiological traits - Storage substances
 GO:0020037 - heme binding
GO:0019825 - oxygen binding
GO:0015671 - oxygen transport
GO:0009790 - embryonic development
 TO:0002653 - endosperm storage protein content
 -
HAP3D OsHAP3D
OsEnS-83
OsNF-YB9
NF-YB9
NFYB9
OsLEC1A
LEC1A
 HAP3D SUBUNIT OF CCAAT-BOX BINDING COMPLEX HAP3 subunit D
LEC1-type 3 subunit protein-D
endosperm-specific gene 83
NUCLEAR FACTOR-Y subunit B9
NUCLEAR FACTOR-Y subunit NF-YB9
HAP3 SUBUNIT D
NF-YB subunit 9
NF-YB family 9
 6 Reproductive organ - Heading date
Reproductive organ - Spikelet, flower, glume, awn
Seed - Physiological traits - Storage substances
Seed - Morphological traits - Endosperm
Tolerance and resistance - Stress tolerance
Other
Seed - Morphological traits - Grain shape
Character as QTL - Plant growth activity
Character as QTL - Grain quality
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0010581 - regulation of starch biosynthetic process
GO:0048316 - seed development
GO:0006350 - transcription
GO:0042127 - regulation of cell proliferation
GO:0006355 - regulation of transcription, DNA-dependent
GO:0009790 - embryonic development
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0043565 - sequence-specific DNA binding
GO:0005737 - cytoplasm
GO:0009845 - seed germination
 TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000146 - seed length
TO:0000149 - seed width
TO:0000304 - seed thickness
TO:0000266 - chalky endosperm
TO:0000391 - seed size
TO:0000399 - grain thickness
TO:0000734 - grain length
TO:0020033 - glume length
TO:0000487 - endosperm color
TO:0000575 - endosperm related trait
TO:0000064 - embryo related trait
TO:0000485 - sterility related trait
TO:0000196 - amylose content
TO:0000696 - starch content
TO:0000276 - drought tolerance
TO:0000211 - gel consistency
TO:0000162 - seed quality
TO:0000222 - head rice
TO:0000207 - plant height
TO:0000382 - 1000-seed weight
TO:0000346 - tiller number
TO:0000639 - seed fertility
TO:0000421 - pollen fertility
 PO:0001170 - seed development stage
PO:0009009 - plant embryo
PO:0009089 - endosperm
PO:0020094 - plant egg cell
PO:0000003 - whole plant
PO:0009010 - seed
Os06g0285200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g17480.1
LEC1 OsHAP3E
HAP3E
OsLEC1/OsHAP3E
OsLEC1
LEC1
OsNF-YB7
NF-YB7
NFYB7
L1L
OsLEC1B
LEC1B
 LEAFY COTYLEDON 1 HAP3 subunit E
LEC1-type 3 subunit protein-E
leafy cotyledon 1
NUCLEAR FACTOR-Y subunit B7
NUCLEAR FACTOR-Y subunit NF-YB7
LEC1-LIKE
LEAFY COTYLEDON1-LIKE
HAP3 SUBUNIT E
NF-YB subunit 7
NF-YB family 7
LEAFY COTYLEDON1
 2 Coloration - Chlorophyll
Character as QTL - Germination
Reproductive organ - Heading date
Seed - Morphological traits - Embryo
Tolerance and resistance - Stress tolerance
Other
Seed - Physiological traits - Dormancy
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0009790 - embryonic development
GO:0010109 - regulation of photosynthesis
GO:0048700 - acquisition of desiccation tolerance
GO:0010099 - regulation of photomorphogenesis
GO:0010115 - regulation of abscisic acid biosynthetic process
GO:0010187 - negative regulation of seed germination
GO:0009269 - response to desiccation
GO:0010371 - regulation of gibberellin biosynthetic process
GO:0010431 - seed maturation
GO:0048316 - seed development
GO:0015995 - chlorophyll biosynthetic process
GO:0009734 - auxin mediated signaling pathway
GO:0043565 - sequence-specific DNA binding
GO:0009740 - gibberellic acid mediated signaling
GO:0009733 - response to auxin stimulus
GO:0008284 - positive regulation of cell proliferation
GO:0048579 - negative regulation of long-day photoperiodism, flowering
GO:0005634 - nucleus
GO:0006355 - regulation of transcription, DNA-dependent
GO:0006350 - transcription
GO:0009738 - abscisic acid mediated signaling
GO:0015979 - photosynthesis
GO:0009845 - seed germination
 TO:0000430 - germination rate
TO:0000428 - callus induction
TO:0000397 - grain size
TO:0000653 - seed development trait
TO:0000137 - days to heading
TO:0000163 - auxin sensitivity
TO:0000620 - embryo development trait
TO:0000391 - seed size
TO:0002661 - seed maturation
TO:0000276 - drought tolerance
TO:0000485 - sterility related trait
TO:0000064 - embryo related trait
TO:0000495 - chlorophyll content
TO:0000207 - plant height
TO:0000488 - seed composition based quality trait
 PO:0001170 - seed development stage
PO:0007057 - 0 seed germination stage
PO:0007631 - plant embryo stage
PO:0009010 - seed
PO:0020110 - scutellum
PO:0005421 - parenchyma
PO:0009009 - plant embryo
PO:0005052 - plant callus
PO:0007632 - seed maturation stage
Os02g0725700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g49370.1
LOC_Os02g49370.2
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