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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
DLC1 RR24
OsRR24
Rrb2
Orr4
OsRR17
RR17
OsRRB2
RRB2
OsRR24/LEPTO1
OsLEPTO1
LEPTO1
OsDLC1
 DEFECTIVE LEPTOTENE CHROMOSOME 1 B-type response regulator 4
B-type RR 2
LEPTOTENE1
LEPTOTENE 1
Defective Leptotene Chromosome 1
 2 Reproductive organ - Pollination, fertilization, fertility - Sterility
Heterochrony
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Tolerance and resistance - Stress tolerance
 GO:0009735 - response to cytokinin stimulus
GO:0009753 - response to jasmonic acid stimulus
GO:0009409 - response to cold
GO:0052543 - callose deposition in cell wall
GO:0045449 - regulation of transcription
GO:0000156 - two-component response regulator activity
GO:0000160 - two-component signal transduction system (phosphorelay)
GO:0009737 - response to abscisic acid stimulus
GO:0009414 - response to water deprivation
GO:0045893 - positive regulation of transcription, DNA-dependent
GO:0009554 - megasporogenesis
GO:0048653 - anther development
GO:0012501 - programmed cell death
GO:0009555 - pollen development
GO:0000237 - leptotene
GO:0009736 - cytokinin mediated signaling
GO:0051276 - chromosome organization
GO:0042138 - meiotic DNA double-strand break formation
GO:0005634 - nucleus
 TO:0000615 - abscisic acid sensitivity
TO:0000167 - cytokinin sensitivity
TO:0000276 - drought tolerance
TO:0000172 - jasmonic acid sensitivity
TO:0000485 - sterility related trait
TO:0000303 - cold tolerance
 PO:0009047 - stem
PO:0009049 - inflorescence
PO:0009005 - root
PO:0009013 - portion of meristem tissue
PO:0025313 - tapetum
PO:0009009 - plant embryo
Os02g0182100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g08500.1
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
CSA csa
OsCSA
MYB2-5
OsMYB2-5
 CARBON STARVED ANTHER R2R3-MYB transcription factor 2-5
 1 Reproductive organ - Pollination, fertilization, fertility - Sterility
Tolerance and resistance - Stress tolerance
Biochemical character
Reproductive organ - Pollination, fertilization, fertility - Male sterility
 GO:0006109 - regulation of carbohydrate metabolic process
GO:0048572 - short-day photoperiodism
GO:0009555 - pollen development
GO:0009742 - brassinosteroid mediated signaling
GO:0048653 - anther development
GO:0009648 - photoperiodism
GO:0009408 - response to heat
GO:0008643 - carbohydrate transport
GO:0009651 - response to salt stress
GO:0003700 - transcription factor activity
GO:0009414 - response to water deprivation
GO:0005634 - nucleus
 TO:0006001 - salt tolerance
TO:0000696 - starch content
TO:0000421 - pollen fertility
TO:0002677 - brassinosteroid sensitivity
TO:0000229 - photoperiod sensitivity
TO:0000276 - drought tolerance
TO:0000259 - heat tolerance
TO:0000009 - genic male sterility-photoperiod sensitive
 PO:0001007 - pollen development stage
PO:0001004 - anther development stage
Os01g0274800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g16810.1
MLS1 mls1
 MALFORMED LEMMA 1 malformed lemma1
malformed lemma 1
malformed lemma-1
 Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0007275 - multicellular organismal development
 TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000436 - spikelet sterility
TO:0000053 - pollen sterility
 PO:0020091 - obsolete microgametophyte
PO:0009038 - palea
PO:0009037 - lemma
PO:0009051 - spikelet
-
MLS2 mls2
 MALFORMED LEMMA 2 malformed lemma2
malformed lemma 2
malformed lemma-2
 Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0007275 - multicellular organismal development
 TO:0000053 - pollen sterility
TO:0000436 - spikelet sterility
TO:0000079 - lemma and palea anatomy and morphology trait
 PO:0020091 - obsolete microgametophyte
PO:0009051 - spikelet
PO:0009038 - palea
PO:0009037 - lemma
-
SUG1 Su g1
 SUPPRESSOR FOR LONG STERILE LEMMAS G 1 Suppressor for long sterile lemmas (g1)
SUPPRESSOR FOR LONG STERILE LEMMAS G1
 Reproductive organ - Spikelet, flower, glume, awn
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0007275 - multicellular organismal development
 TO:0000240 - sterile lemma length
 PO:0009037 - lemma
-
MLS3 mls3
 MALFORMED LEMMA 3 malformed spikelet3 (lemma3 ?)
malformed spikelet 3
malformed spikelet-3
 4 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Spikelet, flower, glume, awn
 GO:0007275 - multicellular organismal development
 TO:0000432 - temperature response trait
TO:0000436 - spikelet sterility
TO:0000079 - lemma and palea anatomy and morphology trait
 PO:0009037 - lemma
PO:0009038 - palea
PO:0009051 - spikelet
PO:0000003 - whole plant
-
SHL2 shl2
SHL2
sh2
OsRDR6
RDR6
DEL
OsDEL
 SHOOTLESS 2 shootless 2
shootless-2
Probable RNA-dependent RNA polymerase SHL2
Protein SHOOTLESS 2
SHOOTLESS2
RNA-dependent RNA polymerase 6
rod-like lemma
DEGENERATED LEMMA
 1 Tolerance and resistance - Disease resistance
Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Tolerance and resistance - Stress tolerance
Seed - Morphological traits - Embryo
Seed - Morphological traits - Grain shape
Character as QTL - Yield and productivity
Vegetative organ - Shoot apical meristem(SAM)
Reproductive organ - Spikelet, flower, glume, awn
 GO:0042742 - defense response to bacterium
GO:0009408 - response to heat
GO:0010093 - specification of floral organ identity
GO:0010229 - inflorescence development
GO:0051607 - defense response to virus
GO:0006950 - response to stress
GO:0009266 - response to temperature stimulus
GO:0009737 - response to abscisic acid stimulus
GO:0030422 - production of siRNA involved in RNA interference
GO:0031047 - gene silencing by RNA
GO:0003723 - RNA binding
GO:0003968 - RNA-directed RNA polymerase activity
GO:0005739 - mitochondrion
GO:0009888 - tissue development
GO:0016246 - RNA interference
GO:0009887 - organ morphogenesis
GO:0042138 - meiotic DNA double-strand break formation
GO:0006306 - DNA methylation
GO:0010492 - maintenance of shoot apical meristem identity
 TO:0000274 - floret anatomy and morphology trait
TO:0000557 - secondary branch number
TO:0000455 - seed set percent
TO:0000622 - flower development trait
TO:0000402 - grain width
TO:0000734 - grain length
TO:0002718 - awn anatomy and morphology trait
TO:0000614 - lemma shape
TO:0000259 - heat tolerance
TO:0000975 - grain width
TO:0000605 - hydrogen peroxide content
TO:0000175 - bacterial blight disease resistance
TO:0000567 - tiller angle
TO:0000040 - panicle length
TO:0000148 - viral disease resistance
TO:0000657 - spikelet anatomy and morphology trait
TO:0002759 - grain number
TO:0000615 - abscisic acid sensitivity
TO:0000396 - grain yield
TO:0000485 - sterility related trait
TO:0000592 - 1000-dehulled grain weight
TO:0000064 - embryo related trait
TO:0000207 - plant height
TO:0000621 - inflorescence development trait
TO:0000164 - stress trait
TO:0000432 - temperature response trait
TO:0000382 - 1000-seed weight
TO:0002730 - grain shape
 PO:0020144 - apical meristem
PO:0009051 - spikelet
PO:0009082 - spikelet floret
PO:0001083 - inflorescence development stage
PO:0009009 - plant embryo
Os01g0527600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g34350.1
image Id ( 6807 )
AID1 aid1
OsAID1
DLN159
OsDLN159
OsMYBR57
MYBR57
 ANTHER INDEHISCENCE 1 anther indehiscence-1
Anther Indehiscence1
DLN repressor 159
DLN motif protein 159
MYB-related protein 57
 6 Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0009414 - response to water deprivation
GO:0003677 - DNA binding
GO:0003700 - transcription factor activity
GO:0005634 - nucleus
GO:0009901 - anther dehiscence
GO:0010152 - pollen maturation
GO:0045449 - regulation of transcription
GO:0043067 - regulation of programmed cell death
 TO:0000437 - male sterility
TO:0000053 - pollen sterility
TO:0000346 - tiller number
TO:0000276 - drought tolerance
TO:0000137 - days to heading
TO:0000245 - pollen free
TO:0000436 - spikelet sterility
 PO:0020002 - anther wall endothecium
PO:0000030 - septum
PO:0009025 - vascular leaf
PO:0020101 - stomium
Os06g0181300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g08290.1
EXPB2 OsEXPB2
OsaEXPb1.9
EXPb1.9
 BETA-EXPANSIN 2 Expansin-B2
Beta-expansin-2
 10 Reproductive organ - Pollination, fertilization, fertility - Sterility
Biochemical character
 GO:0016023 - cytoplasmic membrane-bounded vesicle
GO:0007047 - cell wall organization
GO:0005618 - cell wall
GO:0019898 - extrinsic to membrane
GO:0005576 - extracellular region
GO:0019953 - sexual reproduction
 TO:0000485 - sterility related trait
 Os10g0555700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g40710.1
S33 S33(t)
 GAMETE ELIMINATOR33(T) gamete eliminator33(t)
 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Hybrid sterility
 GO:0007275 - multicellular organismal development
 TO:0000053 - pollen sterility
TO:0000416 - embryosac abortion
TO:0000036 - hybrid incompatibility
TO:0000218 - pollen abortion type
 -
SNB AP2/EREBP#073
AP2/EREBP73
AP2-3
OsAP2-3
SSH1
OsSSH1
OsSNB
DLN181
DLN181a
DLN181b
OsDLN181
OsDLN181a
OsDLN181b
SUI4
OsSUI4
SUI4/SNB
 SUPERNUMERARY BRACT GENE Supernumerary Bract gene
Supernumerary Bract
SUPERNUMERARY BRACT
supernumerary bract
transcription factor; SNB
APETALA2/ethylene-responsive element binding protein 73
APETALA2-3
suppression of shattering1
DLN repressor 181
DLN motif protein 181
shortened uppermost internode 4
 7 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - panicle
Character as QTL - Yield and productivity
Seed - Physiological traits - Shattering
Reproductive organ - Spikelet, flower, glume, awn
Seed - Morphological traits
Seed - Morphological traits - Grain shape
Vegetative organ - Culm
 GO:0009908 - flower development
GO:0009809 - lignin biosynthetic process
GO:0003700 - transcription factor activity
GO:0010022 - meristem determinacy
GO:0010077 - maintenance of inflorescence meristem identity
GO:0010092 - specification of organ identity
GO:0005634 - nucleus
GO:0048506 - regulation of timing of meristematic phase transition
GO:0045449 - regulation of transcription
GO:0080006 - internode patterning
GO:0009740 - gibberellic acid mediated signaling
GO:0009736 - cytokinin mediated signaling
GO:0001558 - regulation of cell growth
GO:0009832 - plant-type cell wall biogenesis
 TO:0000382 - 1000-seed weight
TO:0000733 - lignin biosynthesis trait
TO:0000731 - lignin content
TO:0002729 - fruit senescing quality trait
TO:0000473 - grain shattering
TO:0000391 - seed size
TO:0000590 - grain weight
TO:0000396 - grain yield
TO:0000734 - grain length
TO:0000397 - grain size
TO:0000622 - flower development trait
TO:0000650 - lemma length
TO:0000208 - lemma number
TO:0000499 - flower anatomy and morphology trait
TO:0000145 - internode length
TO:0000207 - plant height
TO:0000225 - stamen number
TO:0006030 - spikelet meristem identity
TO:0006032 - panicle size
TO:0000436 - spikelet sterility
TO:0000209 - palea number
TO:0000671 - pre-flowering flower abortion
 PO:0009029 - stamen
PO:0006327 - spikelet meristem
PO:0009030 - carpel
PO:0009036 - lodicule
PO:0009039 - glume
PO:0007615 - flower development stage
PO:0009034 - flower bract
Os07g0235800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g13170.2
LOC_Os07g13170.1
KU70 OsKu70
Ku70
 _ rice homolog of Ku70
Ku70 homolog
 7 Reproductive organ - Pollination, fertilization, fertility - Sterility
Biochemical character
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Tolerance and resistance - Stress tolerance
 GO:0005524 - ATP binding
GO:0042162 - telomeric DNA binding
GO:0032502 - developmental process
GO:0009408 - response to heat
GO:0043564 - Ku70:Ku80 complex
GO:0003690 - double-stranded DNA binding
GO:0006281 - DNA repair
GO:0006303 - double-strand break repair via nonhomologous end joining
GO:0006310 - DNA recombination
GO:0004003 - ATP-dependent DNA helicase activity
GO:0003684 - damaged DNA binding
GO:0000723 - telomere maintenance
 TO:0000168 - abiotic stress trait
TO:0000485 - sterility related trait
TO:0000357 - growth and development trait
 Os07g0184900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g08729.1
RAD51D OsRAD51D
OsRad51D
OsRAD51D.1
OsRAD51D.2
OsRAD51D.3
 DNA REPAIR PROTEIN RAD51D DNA repair protein RAD51D
 9 Reproductive organ - Pollination, fertilization, fertility - Sterility
Biochemical character
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Spikelet, flower, glume, awn
 GO:0007130 - synaptonemal complex assembly
GO:0022414 - reproductive process
GO:0000723 - telomere maintenance
GO:0007126 - meiosis
GO:0010332 - response to gamma radiation
GO:0045002 - double-strand break repair via single-strand annealing
GO:0045003 - double-strand break repair via synthesis-dependent strand annealing
GO:0006302 - double-strand break repair
GO:0007129 - synapsis
 TO:0000079 - lemma and palea anatomy and morphology trait
TO:0000485 - sterility related trait
TO:0000161 - radiation response trait
TO:0000225 - stamen number
 Os09g0104200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g01680.1
LOC_Os09g01680.2
LOC_Os09g01680.3
BGLU5 Os1bglu5
Os1Bglu5
1bglu5
 BETA-GLUCOSIDASE 5 beta-glucosidase 5
 1 Reproductive organ - Heading date
Reproductive organ - Pollination, fertilization, fertility - Sterility
Biochemical character
 GO:0005975 - carbohydrate metabolic process
GO:0008422 - beta-glucosidase activity
GO:0048573 - photoperiodism, flowering
 TO:0000485 - sterility related trait
TO:0000137 - days to heading
 Os01g0930800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g70520.1
LOC_Os01g70520.2
DRM2 OsDRM2
osdrm2
DRM2-1
 DOMAINS REARRANGED METHYLTRANSFERASE 2 domains rearranged methyltransferase 2
domains rearranged methylase 2
 3 Reproductive organ - panicle
Character as QTL - Plant growth activity
Reproductive organ - Spikelet, flower, glume, awn
Vegetative organ - Culm
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Heading date
Biochemical character
 GO:0050832 - defense response to fungus
GO:0006306 - DNA methylation
GO:0006346 - methylation-dependent chromatin silencing
GO:0009651 - response to salt stress
GO:0051567 - histone H3-K9 methylation
GO:0010426 - DNA methylation on cytosine within a CHH sequence
GO:0010425 - DNA methylation on cytosine within a CNG sequence
GO:0003677 - DNA binding
GO:0046686 - response to cadmium ion
GO:0008168 - methyltransferase activity
 TO:0000357 - growth and development trait
TO:0006001 - salt tolerance
TO:0000262 - panicle shape
TO:0002616 - flowering time
TO:0000207 - plant height
TO:0000657 - spikelet anatomy and morphology trait
TO:0000346 - tiller number
TO:0000485 - sterility related trait
 Os03g0110800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g02010.4
CMT2 OsCMT2
OsCMT3a
CMT3a
 CHROMOMETHYLTRANSFERASE 2 chromomethyltransferase 2
chromomethylase 3a
CHG methyltransferase 3a
 10 Tolerance and resistance - Stress tolerance
Character as QTL - Plant growth activity
Biochemical character
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0006346 - methylation-dependent chromatin silencing
GO:0051567 - histone H3-K9 methylation
GO:0010426 - DNA methylation on cytosine within a CHH sequence
GO:0006342 - chromatin silencing
GO:0009294 - DNA mediated transformation
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity
GO:0010069 - zygote asymmetric cytokinesis in the embryo sac
GO:0003677 - DNA binding
GO:0010425 - DNA methylation on cytosine within a CNG sequence
GO:0006306 - DNA methylation
GO:0032502 - developmental process
GO:0032776 - DNA methylation on cytosine
GO:0070895 - negative regulation of transposon integration
GO:0005634 - nucleus
GO:0032196 - transposition
GO:0009008 - DNA-methyltransferase activity
GO:0009555 - pollen development
GO:0046686 - response to cadmium ion
 TO:0000357 - growth and development trait
TO:0000485 - sterility related trait
TO:0000421 - pollen fertility
 PO:0020094 - plant egg cell
PO:0001007 - pollen development stage
PO:0000423 - plant zygote
Os10g0104900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g01570.1
_ OsWD40-17
OsLUGL
LUGL
KKX
OsKKX
 _ LEUNIG-like transcriptional regulator
KAIKOUXIAO
LEUNIG-like
LEUNIG
 1 Reproductive organ - Pollination, fertilization, fertility - Sterility
Seed - Morphological traits
Reproductive organ - panicle
Reproductive organ - Spikelet, flower, glume, awn
 GO:0048449 - floral organ formation
GO:0005634 - nucleus
GO:0010229 - inflorescence development
GO:0009908 - flower development
GO:0009734 - auxin mediated signaling pathway
 TO:0000184 - seed anatomy and morphology trait
TO:0000485 - sterility related trait
TO:0000621 - inflorescence development trait
TO:0002672 - auxin content
 PO:0006327 - spikelet meristem
PO:0025127 - primordium
PO:0025477 - floral organ primordium
PO:0000229 - flower meristem
PO:0001083 - inflorescence development stage
Os01g0607400 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g42260.4
LOC_Os01g42260.3
LOC_Os01g42260.2
LOC_Os01g42260.1
PAIR1 Pair1
OsPAIR1
 HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 1 HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1
Homologous pairing aberration in rice meiosis 1
Protein PAIR1
Protein HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 1
 3 Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0005634 - nucleus
GO:0007128 - meiotic prophase I
GO:0007133 - meiotic anaphase I
GO:0007134 - meiotic telophase I
GO:0009556 - microsporogenesis
GO:0009554 - megasporogenesis
 TO:0000358 - female sterility
TO:0000729 - meiotic cell cycle trait
TO:0000437 - male sterility
 PO:0020047 - microsporocyte
PO:0000431 - megasporocyte
Os03g0106300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g01590.1
LOC_Os03g01590.2
ZIP4 OsZIP4
SPO22
OsSPO22
 _ ZMM protein OsZIP4
rice ZIP4 homolog
 1 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
 GO:0000712 - resolution of meiotic joint molecules as recombinants
GO:0007126 - meiosis
GO:0007143 - female meiosis
GO:0009507 - chloroplast
GO:0005634 - nucleus
GO:0005694 - chromosome
GO:0007140 - male meiosis
GO:0007131 - reciprocal meiotic recombination
GO:0007129 - synapsis
 Os01g0890900 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g66690.1
BRK1 BUB1-RELATED KINASE 1
 OsBRK1 Bub1-related kinase 1
 7 Reproductive organ - Pollination, fertilization, fertility - Sterility
Biochemical character
Reproductive organ - Pollination, fertilization, fertility - Male sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
 GO:0030036 - actin cytoskeleton organization
GO:0006468 - protein amino acid phosphorylation
GO:0007053 - spindle assembly involved in male meiosis
GO:0005829 - cytosol
GO:0007094 - mitotic cell cycle spindle assembly checkpoint
GO:0018105 - peptidyl-serine phosphorylation
GO:0000776 - kinetochore
GO:0045144 - meiotic sister chromatid segregation
GO:0007126 - meiosis
GO:0018107 - peptidyl-threonine phosphorylation
GO:0051323 - metaphase
GO:0004674 - protein serine/threonine kinase activity
GO:0005524 - ATP binding
GO:0007067 - mitosis
 TO:0000485 - sterility related trait
TO:0000437 - male sterility
 Os07g0508500 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g32480.1
RPA2C RPA2c
OsRPA2c
 REPLICATION PROTEIN A 2C Replication Protein A2c
 6 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
 GO:0005634 - nucleus
GO:0003677 - DNA binding
GO:0006310 - DNA recombination
GO:0006281 - DNA repair
GO:0006260 - DNA replication
 Os06g0693300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g47830.1
RBP-P OsRBP-P
RRM1-4
OsRRM1-4
 RNA-BINDING PROTEIN P RNA binding protein P
RNA recognition motif domain protein 1-4
 1 Vegetative organ - Culm
Reproductive organ - Heading date
Seed - Morphological traits
Reproductive organ - Pollination, fertilization, fertility - Sterility
Other
Seed - Physiological traits - Storage substances
 GO:0048316 - seed development
GO:0000166 - nucleotide binding
GO:0008380 - RNA splicing
GO:0006403 - RNA localization
GO:0005829 - cytosol
GO:0016197 - endosome transport
GO:0016071 - mRNA metabolic process
GO:0010431 - seed maturation
GO:0005634 - nucleus
GO:0005737 - cytoplasm
GO:0005768 - endosome
GO:0003676 - nucleic acid binding
GO:0051028 - mRNA transport
GO:0048573 - photoperiodism, flowering
GO:0009845 - seed germination
 TO:0000346 - tiller number
TO:0000495 - chlorophyll content
TO:0000207 - plant height
TO:0002653 - endosperm storage protein content
TO:0000397 - grain size
TO:0000137 - days to heading
TO:0000485 - sterility related trait
TO:0002616 - flowering time
TO:0002661 - seed maturation
TO:0000180 - spikelet fertility
 PO:0007632 - seed maturation stage
Os01g0265800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g16090.1
MFS1 MND1
OsMND1
OsMFS1
 MALE AND FEMALE STERILITY 1 male and female sterility 1
meiotic nuclear division protein 1
 9 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Biochemical character
 GO:0006302 - double-strand break repair
GO:0048232 - male gamete generation
GO:0048653 - anther development
GO:0005634 - nucleus
GO:0000724 - double-strand break repair via homologous recombination
GO:0060542 - regulation of strand invasion
GO:0009555 - pollen development
GO:0009553 - embryo sac development
 TO:0000416 - embryosac abortion
TO:0000729 - meiotic cell cycle trait
TO:0000218 - pollen abortion type
TO:0000455 - seed set percent
TO:0000485 - sterility related trait
TO:0000358 - female sterility
TO:0000437 - male sterility
 PO:0007616 - flowering stage
PO:0001004 - anther development stage
Os09g0280600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os09g10850.1
MEICA1 MEIOTIC CHROMOSOME ASSOCIATION 1 Meiotic Chromosome Association 1
 3 Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0045132 - meiotic chromosome segregation
GO:0000710 - meiotic mismatch repair
GO:0010520 - regulation of reciprocal meiotic recombination
 TO:0000180 - spikelet fertility
TO:0000485 - sterility related trait
TO:0000421 - pollen fertility
 Os03g0144000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g05040.1
SHOC1 OsSHOC1
 SHORTAGE IN CHIASMATA 1 Shortage in chiasmata 1
 2 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
 GO:0000712 - resolution of meiotic joint molecules as recombinants
GO:0007131 - reciprocal meiotic recombination
 TO:0000485 - sterility related trait
 Os02g0642600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g42910.1
PTD1 OsPTD1
 PARTING DANCER 1 Parting Dancer 1
 5 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Pollination, fertilization, fertility - Meiosis
 GO:0007140 - male meiosis
GO:0000712 - resolution of meiotic joint molecules as recombinants
GO:0009555 - pollen development
GO:0048236 - plant-type spore development
GO:0010845 - positive regulation of reciprocal meiotic recombination
 TO:0000485 - sterility related trait
 Os05g0588200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g51060.1
MTA2 OsMTA2
OsIME4
IME4
OsMTB
MTB
 MRNA ADENOSINE METHYLASE 2 mRNA adenosine methylase 2
inducer of meiosis 4
OsIME4 sense transcript
RNA methyltransferase B
 2 Tolerance and resistance - Disease resistance
Tolerance and resistance - Stress tolerance
Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Pollination, fertilization, fertility - Sterility
Seed - Morphological traits - Embryo
Biochemical character
 GO:0009555 - pollen development
GO:0001100 - negative regulation of exit from mitosis
GO:0000278 - mitotic cell cycle
GO:0045995 - regulation of embryonic development
GO:0005634 - nucleus
GO:0016607 - nuclear speck
GO:0042742 - defense response to bacterium
GO:0050832 - defense response to fungus
GO:0009409 - response to cold
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0009269 - response to desiccation
GO:0009611 - response to wounding
GO:0003723 - RNA binding
GO:0008168 - methyltransferase activity
GO:0001510 - RNA methylation
GO:0009793 - embryonic development ending in seed dormancy
GO:0080009 - mRNA methylation
GO:0009507 - chloroplast
 TO:0000303 - cold tolerance
TO:0000175 - bacterial blight disease resistance
TO:0000357 - growth and development trait
TO:0000620 - embryo development trait
TO:0000180 - spikelet fertility
TO:0000040 - panicle length
TO:0006001 - salt tolerance
TO:0000276 - drought tolerance
TO:0000315 - bacterial disease resistance
TO:0000439 - fungal disease resistance
TO:0000730 - mitotic cell cycle trait
TO:0000074 - blast disease
TO:0000392 - sterility or fertility trait
 PO:0007631 - plant embryo stage
PO:0001007 - pollen development stage
PO:0020003 - plant ovule
PO:0009066 - anther
Os02g0672600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g45110.1
CHR721 OsCHR721
SMARCAL1
OsSMARCAL1
 CHROMATIN REMODELING FACTOR 721 chromatin remodeling factor 721
 7 Tolerance and resistance - Stress tolerance
Tolerance and resistance - Disease resistance
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0009554 - megasporogenesis
GO:0050832 - defense response to fungus
GO:0006281 - DNA repair
GO:0005634 - nucleus
GO:0031297 - replication fork processing
GO:0043596 - nuclear replication fork
GO:0006974 - response to DNA damage stimulus
GO:0006338 - chromatin remodeling
GO:0003678 - DNA helicase activity
GO:0005524 - ATP binding
GO:0008094 - DNA-dependent ATPase activity
GO:0048478 - replication fork protection
GO:0009651 - response to salt stress
GO:0009414 - response to water deprivation
GO:0009555 - pollen development
GO:0007135 - meiosis II
 TO:0000074 - blast disease
TO:0000276 - drought tolerance
TO:0006001 - salt tolerance
TO:0000485 - sterility related trait
 PO:0009051 - spikelet
PO:0001007 - pollen development stage
Os07g0636200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os07g44210.1
SPL OsSPL
 SPOROCYTELESS 5 Reproductive organ - Pollination, fertilization, fertility - Meiosis
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0052545 - callose localization
GO:0051728 - cell cycle switching, mitotic to meiotic cell cycle
GO:0006325 - chromatin organization
GO:0009554 - megasporogenesis
 TO:0000485 - sterility related trait
 Os05g0501800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os05g42240.1
_ _ 1 Reproductive organ - Pollination, fertilization, fertility - Sterility
Vegetative organ - Culm
 TO:0000485 - sterility related trait
TO:0000207 - plant height
 Os01g0884200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 )
_ _ 1 Reproductive organ - Heading date
Character as QTL - Yield and productivity
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0048573 - photoperiodism, flowering
 TO:0000346 - tiller number
TO:0000485 - sterility related trait
TO:0000137 - days to heading
 Os01g0886000 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os01g66280.1
_ _ 10 Vegetative organ - Culm
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0000967 - rRNA 5'-end processing
 TO:0000485 - sterility related trait
TO:0000207 - plant height
 Os10g0555200 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g40650.1
DLN239 OsDLN239
 DLN REPRESSOR 239 DLN repressor 239
DLN motif protein 239
 10 Vegetative organ - Culm
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0003676 - nucleic acid binding
 TO:0000485 - sterility related trait
TO:0000207 - plant height
 Os10g0555300 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g40660.1
TRFL1 OsTRFL1
 TELOMERE REPEAT-BINDING FACTOR LIKE 1 telomere repeat-binding factor like 1
 2 Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0032502 - developmental process
GO:0003677 - DNA binding
GO:0000723 - telomere maintenance
 TO:0000485 - sterility related trait
 PO:0025034 - leaf
PO:0009006 - shoot system
PO:0009010 - seed
PO:0005052 - plant callus
Os02g0776700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g53670.1
LOC_Os02g53670.2
LOC_Os02g53670.3
LOC_Os02g53670.4
_ OsGME2
GME2
 _ GDP-D-mannose epimerase 2
 11 Character as QTL - Yield and productivity
Biochemical character
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0005829 - cytosol
GO:0051287 - NAD or NADH binding
GO:0019853 - L-ascorbic acid biosynthetic process
GO:0047918 - GDP-mannose 3,5-epimerase activity
 TO:0000448 - filled grain percentage
TO:0000382 - 1000-seed weight
TO:0000436 - spikelet sterility
TO:0000371 - yield trait
 Os11g0591100 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os11g37890.1
LOC_Os11g37890.2
LOC_Os11g37890.3
_ OsGME1
GME1
 _ GDP-D-mannose-3'
5'-epimerase 1
GDP-D-mannose epimerase 1
 10 Character as QTL - Yield and productivity
Tolerance and resistance - Stress tolerance
Biochemical character
Tolerance and resistance - Disease resistance
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0050832 - defense response to fungus
GO:0050662 - coenzyme binding
GO:0010043 - response to zinc ion
GO:0019853 - L-ascorbic acid biosynthetic process
GO:0047918 - GDP-mannose 3,5-epimerase activity
 TO:0000448 - filled grain percentage
TO:0000074 - blast disease
TO:0000371 - yield trait
TO:0000382 - 1000-seed weight
TO:0000351 - zinc sensitivity
TO:0000436 - spikelet sterility
 Os10g0417600 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os10g28200.1
LOC_Os10g28200.2
ORP1C OsORP1C
 OXYSTEROL-BINDING RELATED PROTEIN 1C oxysterol-binding related protein 1C
OSBP-related protein 1C
oxysterol-binding protein-related protein 1C
 3 Character as QTL - Yield and productivity
Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Heading date
Character as QTL - Plant growth activity
Tolerance and resistance - Disease resistance
 GO:0042742 - defense response to bacterium
GO:0002237 - response to molecule of bacterial origin
GO:0008289 - lipid binding
 TO:0000137 - days to heading
TO:0000175 - bacterial blight disease resistance
TO:0000357 - growth and development trait
TO:0000371 - yield trait
TO:0000207 - plant height
TO:0000485 - sterility related trait
TO:0000455 - seed set percent
 Os03g0704700 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os03g49770.2
LOC_Os03g49770.1
FAH OsFAH
 FUMARYLACETOACETATE HYDROLASE Fumarylacetoacetate hydrolase
 2 Seed - Morphological traits - Embryo
Biochemical character
Seed - Morphological traits - Endosperm
Reproductive organ - Pollination, fertilization, fertility - Sterility
 GO:0046872 - metal ion binding
GO:0006559 - L-phenylalanine catabolic process
GO:0006572 - tyrosine catabolic process
GO:0005829 - cytosol
GO:0009790 - embryonic development
GO:0004334 - fumarylacetoacetase activity
GO:0008219 - cell death
 TO:0000447 - filled grain number
TO:0000231 - endospermless
TO:0000620 - embryo development trait
TO:0000485 - sterility related trait
TO:0000189 - embryoless
 PO:0009073 - stigma
PO:0009049 - inflorescence
PO:0007633 - endosperm development stage
PO:0007631 - plant embryo stage
PO:0020122 - inflorescence axis
PO:0009046 - flower
PO:0020038 - petiole
PO:0020138 - leaf lamina vein
PO:0003011 - root vascular system
PO:0020100 - hypocotyl
PO:0020030 - cotyledon
PO:0009005 - root
PO:0009067 - filament
PO:0009047 - stem
PO:0025034 - leaf
PO:0009031 - sepal
Os02g0196800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os02g10310.3
LOC_Os02g10310.2
LOC_Os02g10310.1
_ OsSTA181
STA181
OsPMT16
PMT16
 _ pectin methyltransferase 16
 6 Reproductive organ - Pollination, fertilization, fertility - Sterility
Reproductive organ - Spikelet, flower, glume, awn
 GO:0048437 - floral organ development
GO:0045488 - pectin metabolic process
 TO:0000392 - sterility or fertility trait
TO:0006022 - floral organ development trait
TO:0000223 - pistil anatomy and morphology trait
TO:0002610 - pistil length
TO:0002609 - stamen length
 PO:0009030 - carpel
PO:0009066 - anther
PO:0025395 - floral organ
PO:0025585 - floral organ formation stage
Os06g0712800 Oryzabase ( IRGSP 1.0 / Build5 )
Rap ( IRGSP 1.0 / Build5 ) 		LOC_Os06g49860.1
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/rice/oryzabase