Seed development (WP2199)

Oryza sativa

The network features protein-protein interactions related to seed development in rice. Co-expression information for some genes known to be important for seed development is also shown. The Gene Basket contains a few genes/proteins that are known to be important for the process but for which interactions were unknown or intentionally left out when the network was created. Please go ahead and move them into the network if you find the correct interacting partner(s).


Mamatha Hanumappa , Pankaj Jaiswal , Lauren J. Dupuis , Eric Weitz , and Lars Willighagen


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Oryza sativa



Cell Type Ontology

obsolete plant cell

Pathway Ontology

signaling pathway


Label Type Compact URI Comment
HOX 22 GeneProduct :LOC_Os04g45810 In Cooper et al. 2003 protein sequence provided matches HOX 22, however it was named HOX6 (AF145730)
Dynamin GeneProduct :LOC_Os06g13820
IAA amidohydrolase GeneProduct :LOC_Os03g62060
HSP40 GeneProduct :LOC_Os03g44620
bHLH60 GeneProduct :LOC_Os08g04390 Helix-loop-helix TF
MADS 18 GeneProduct :LOC_Os07g41370 Also called MADS 28
PPDKB GeneProduct :LOC_Os05g33570 Involved in grain filling
2-d-3-D phosphooctonate aldolase GeneProduct :LOC_Os12g10784
GB2 GeneProduct :LOC_Os03g57960 Globulin 2
BTB/POZ GeneProduct :LOC_Os10g29390 2-keto-3-deoxy-6-phosphogluconate aldolase
LOC_Os06g39906 GeneProduct :LOC_Os06g39906
NB-ARC domain protein GeneProduct :LOC_Os11g34880 Jacalin
ZF-like GeneProduct :LOC_Os01g40990
grpA3 GeneProduct :LOC_Os05g02780
EXPB4 GeneProduct :LOC_Os10g40730 Beta-expansin-4
Bam 4 GeneProduct :LOC_Os07g47120
Pyrrolidone-Carboxylpeptidase GeneProduct :LOC_Os03g25270
SPS-O spp GeneProduct :LOC_Os08g20660 sucrose-phosphate synthase-Oncidium spp= named after table III on Yamakawa et al. (2007)
IAA4 GeneProduct :LOC_Os01g18360
Cyp2 GeneProduct :LOC_Os02g02890
Bam 7 GeneProduct :LOC_Os03g04770
Thioredoxin-like GeneProduct :LOC_Os04g57310 thiol-disulphide oxidoreductase DCC
Shaggy kinase GeneProduct :LOC_Os10g37740
Pto kinase Interactor 1 GeneProduct :LOC_Os05g04520
LOC_Os09g38090 GeneProduct :LOC_Os09g38090
PCNA GeneProduct :LOC_Os02g56130 Proliferating cell nuclear antigen expressed strongly in the shoot apical meristem
GDSL-like Lipase GeneProduct :LOC_Os10g05088 SGNH_plant_lipase
PP2A-3 GeneProduct :LOC_Os02g12580
TRNA endonuclease GeneProduct :LOC_Os11g38930 catalytic C-terminal domain containing protein
SSIVb GeneProduct :LOC_Os05g45720 Also called ALK
UDP-glucosyl transferase GeneProduct :LOC_Os04g12960
WRKY 51 GeneProduct :LOC_Os04g21950 ABA-inducible & GA-repressible WRKY 51 by itself also represses activation of Amy2A by GAMYB
RSR1 GeneProduct :LOC_Os01g40280
RAD6 GeneProduct :LOC_Os03g57790 transcripts of both OsRad6 and OsSgt1 were found to be strongly expressed in the proliferating tissues such SAM
HAD-like GeneProduct :LOC_Os03g16670
Myosin like GeneProduct :LOC_Os05g02820
SAM cmtr GeneProduct :LOC_Os02g06770
Kinesin GeneProduct :LOC_Os03g43100
SSIIIb GeneProduct :LOC_Os04g53310 Also called ALK
EF-1-d2 GeneProduct :LOC_Os03g29260 Elongation factor 1 beta 2
Keto acyl CoA thiolase GeneProduct :LOC_Os02g57260
OsFBX237 GeneProduct :LOC_Os07g35050 Cdc2-related protein kinase
ZIP-1a GeneProduct :LOC_Os12g13170
eif(iso)4g GeneProduct :LOC_Os04g42140
Fructose-6-phosphate 1-phosphotransferase GeneProduct :LOC_Os08g25720
GluA-3 GeneProduct :LOC_Os03g31360
RAV1-like GeneProduct :LOC_Os01g49830
LEA 14-A GeneProduct :LOC_Os05g50710
GABA permease GeneProduct :LOC_Os01g71720 Amino acid/polyamine transporter
OsIAA13 GeneProduct :LOC_Os03g53150
OSE2 GeneProduct :LOC_Os01g64730 bZIP transcription factor domain containing protein
MAPK2 GeneProduct :LOC_Os02g05480 UniProt:MAPK2, BIMK1, MAP3, MAPK5, MPK3, MSRMK2
IDI2 GeneProduct :LOC_Os11g11050 Initiation factor 2 subunit family protein
AP37 GeneProduct :LOC_Os01g58420
SNAC1 GeneProduct :LOC_Os03g60080
IDS1/ MT4A GeneProduct :LOC_Os12g38270
GBSSII GeneProduct :LOC_Os07g22930 Also called ALK
Ser/thr PK GeneProduct :LOC_Os06g04880
LOC_Os03g50390 GeneProduct :LOC_Os03g50390 Protein Kinase-UniProt ID
PRP1 GeneProduct :LOC_Os05g13940
INV2 GeneProduct :LOC_Os01g22900 Neutral/alkaline invertase 2 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)
Phosphoglucomutase GeneProduct :LOC_Os05g48200
EPSPS1 GeneProduct :LOC_Os06g04280 5-Enolpyruvylshikimate-3-phosphate synthase 1
APL4/ AGPL4 GeneProduct :LOC_Os07g13980
CycD2-2 GeneProduct :LOC_Os07g42860
Amy3A GeneProduct :LOC_Os09g28400
TPR-PK GeneProduct :LOC_Os03g61010 Putative protein kinase
SPS-Zm GeneProduct :LOC_Os06g42824 sucrose-phosphate synthase-Zea mays= named after table III on Yamakawa et al. (2007)
FERTILLIN GeneProduct :LOC_Os06g01650
Disease resistance-like GeneProduct :LOC_Os12g40490 LIM domain-containing protein, putative, expressed
bip129 GeneProduct :LOC_Os08g40790
KOB1 GeneProduct :LOC_Os02g57240 Probable voltage-gated potassium channel subunit beta
GP-alpha-1 GeneProduct :LOC_Os05g26890 G-alpha protein also called GPA1/D1/GA1
DAHPS1 GeneProduct :LOC_Os03g27230 3-deoxy-D-arabino heptulosonate-7-phosphate synthase 1
NAAT1 GeneProduct :LOC_Os02g20360 nicotianamine aminotransferase
NAC5 GeneProduct :LOC_Os11g08210 ABA related
SSIIIa/ Flo5 GeneProduct :LOC_Os08g09230 expression diminished during grain filling at high temperatures
Amy4A GeneProduct :LOC_Os01g51754
NAC2 GeneProduct :LOC_Os02g57650
U2 snRNP GeneProduct :LOC_Os11g41820
SPS-So GeneProduct :LOC_Os06g43630 sucrose-phosphate synthase-Saccharum officinarum= named after table III on Yamakawa et al. (2007)
Pr1b GeneProduct :LOC_Os01g28450
GluA-2 GeneProduct :LOC_Os10g26060
MTN GeneProduct :LOC_Os06g02220 Methylthioadenosine/S-adenosyl homocysteine nucleosidase
RPS20 GeneProduct :LOC_Os06g04290 P35686
Phosphotyrosine GeneProduct :LOC_Os08g44320
Ser/thr PK GeneProduct :LOC_Os02g43290
ZOS1-15 GeneProduct :LOC_Os01g62190 Salt-stress ABA related
MADS7/45 GeneProduct :LOC_Os08g41950 also called MADS 45, AGL6, M79
ARD2 GeneProduct :LOC_Os03g06620 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2; Also called IDI1 and SIP2A
GAMYB GeneProduct :LOC_Os01g59660 regulates GA induction of Amy2A
ALDH7 GeneProduct :LOC_Os09g26880 Needed for seed maturation and viability. Expression Patterns during Seed Development Correspond with Pigment Accumulation Patterns in Seeds Plays a role in the removal of MDA that forms during seed desiccation
DOF ZF GeneProduct :LOC_Os02g49440
WRKY 71 GeneProduct :LOC_Os02g08440 ABA-inducible & GA-repressible Interaction between WRKY 51 and 71 enhances the binding affinity of WRKY71 to the Amy32b promoter WRKY 71 by itself also represses activation of Amy2A by GAMYB
Complex 1L GeneProduct :LOC_Os06g50000 Assigned as Complex 1L by Nemeth D and Hanumappa M (10/21/2010) complex 1 family protein-like (LYR family)
PP2A-B GeneProduct :LOC_Os05g40350
GF14A GeneProduct :LOC_Os08g37490 WIN2, WIP2
PROLM26 GeneProduct :LOC_Os07g10580 Prolamin precursor, also called RP5
MT2b GeneProduct :LOC_Os05g02070
IAA1 GeneProduct :LOC_Os01g08320
LOC_Os01g14110 GeneProduct :LOC_Os01g14110 Assigned as bHLH-tf by Nemeth D and Hanumappa M (10/21/2010)
TAP46 GeneProduct :LOC_Os12g04290
PIT GeneProduct :LOC_Os01g05620
Permease GeneProduct :LOC_Os07g04180
SSII-3 GeneProduct :LOC_Os06g12450 expression diminished during grain filling at high temperatures
SuSy6 GeneProduct :LOC_Os04g24430 Sucrose synthase 6
NAC 10 GeneProduct :LOC_Os11g03300
Myosin like GeneProduct :LOC_Os03g16120
Sub9 GeneProduct :LOC_Os01g58290 Amino acid transporters
DUF630 GeneProduct :LOC_Os10g41310 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)
CACTA, En/Spm GeneProduct :LOC_Os01g09220
CDKA-2 GeneProduct :LOC_Os02g03060
PHT4;3 GeneProduct :LOC_Os01g63290 Na+ dep inorg phosphate cotransporter
Oryzain alpha Protease GeneProduct :LOC_Os04g55650
msrB-1 GeneProduct :LOC_Os03g24600 2 more IDs found on Gramene. Hence called 1, 2 and 3 to differentiate. LOC_Os06g27760=msrB-2, LOC_Os05g33510=msrB-3 (D Nemeth and M Hanumappa 08/17/2010).
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GTP cyclohydrolase GeneProduct :LOC_Os05g38570 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase
Ubiquitin proteinase GeneProduct :LOC_Os02g43760 ubiquitin carboxyl-terminal hydrolase, family 1, putative, expressed
PP2A1 GeneProduct :LOC_Os06g37660
LOC_Os01g62740 GeneProduct :LOC_Os01g62740
Bam 5 GeneProduct :LOC_Os10g32810
AP2 domain GeneProduct :LOC_Os03g64260
SET domain protein GeneProduct :LOC_Os02g40770 histone-lysine N-methyltransferase
UOS1 GeneProduct :LOC_Os06g49120 NAD(P)-binding/Rossman fold
SPK GeneProduct :LOC_Os10g39420 required for storage product accumulation during seed development seed-specific protein kinase
MADS 3 GeneProduct :LOC_Os01g10504 Also called RAG
USP1 GeneProduct :LOC_Os07g47620 ETFP adenine nucleotide
LOC_Os03g56940 GeneProduct :LOC_Os03g56940
GPT2-B GeneProduct :LOC_Os01g07310 Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)
BT1-1 GeneProduct :LOC_Os05g07900
SPS-Hv GeneProduct :LOC_Os02g09170 sucrose-phosphate synthase-Hordeum vulgare= named after table III on Yamakawa et al. (2007)
LPLA GeneProduct :LOC_Os08g33810
NAS2 GeneProduct :LOC_Os03g19420 NA synthase gene 2
GW2 GeneProduct :LOC_Os02g14720 encodes a RING protein with E3 ubiquitin ligase activity
GDSL-like Lipase GeneProduct :LOC_Os01g11650
ARF1 GeneProduct :LOC_Os11g32110
UGP GeneProduct :LOC_Os02g02550
DEP GeneProduct :LOC_Os11g29370 Haloacid dehalogenase-like hydrolase family protein
flavanone 3-hydroxylase GeneProduct :LOC_Os08g37456 2-oxoglutarate (2OG) - Fe(II) oxygenase
BBTI4 GeneProduct :LOC_Os01g03340 Bowman-Birk type bran trypsin inhibitor
HMG1 GeneProduct :LOC_Os06g51220
PPROL 14 E GeneProduct :LOC_Os05g26377 13 kDa Prolamin, also called PPROL 14, PPROL 4A, PPROL 7, PG5a, PROLM 8, PROLM 9, UniProt ID: Q95737
CIN1 GeneProduct :LOC_Os02g33110
ADP ribosylation GTPase GeneProduct :LOC_Os03g17020
MADS 6 GeneProduct :LOC_Os02g45770 Also called MFO1
GLUB4 GeneProduct :LOC_Os02g16830
SuSy4 GeneProduct :LOC_Os03g22120 Sucrose synthase 4
GF14-e GeneProduct :LOC_Os02g36974
CDKA-1 GeneProduct :LOC_Os03g02680
IDEF2 GeneProduct :LOC_Os05g35170 IDE-binding factor 2
SUS1 GeneProduct :LOC_Os03g28330 Sucrose synthase 1
LOC_Os01g12080 GeneProduct :LOC_Os01g12080
Amy3E GeneProduct :LOC_Os08g36900
prx61 GeneProduct :LOC_Os04g59190 Class III peroxidase 61
MADS13 GeneProduct :LOC_Os12g10540 Also called MAF1
SWEET3a GeneProduct :LOC_Os05g12320
BEIII GeneProduct :LOC_Os06g26234
Pectinesterase GeneProduct :LOC_Os07g02810
VIP1-like GeneProduct :LOC_Os06g02240
AREB GeneProduct :LOC_Os05g41070
PPDKA GeneProduct :LOC_Os03g31750 Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)
PUL GeneProduct :LOC_Os04g08270 expression diminished during grain filling at high temperatures
CCT/B-box zinc finger GeneProduct :LOC_Os02g49230
CIN3 GeneProduct :LOC_Os04g33720
TUBB3 GeneProduct :LOC_Os06g46000 Tubulin beta-3 chain
ACO1 GeneProduct :LOC_Os09g27750
SAP11 GeneProduct :LOC_Os08g39450 Also called ZFP60
MADS47 GeneProduct :LOC_Os03g08754 Also called MDP
KRP3 GeneProduct :LOC_Os11g40030
DMAS1 GeneProduct :LOC_Os03g13390 Deoxymugineic acid synthase1
CIN5 GeneProduct :LOC_Os04g56930
LOC_Os03g07360 GeneProduct :LOC_Os03g07360
RIC1 GeneProduct :LOC_Os01g37800
RBCL GeneProduct :LOC_Os10g21268
CIN2 GeneProduct :LOC_Os04g33740
DEK1 GeneProduct :LOC_Os02g48000
RA GeneProduct :LOC_Os04g47080 seed coat color, endosperm color
HSP90 GeneProduct :LOC_Os09g30418 Also called HSP81-2
GF14F GeneProduct :LOC_Os03g50290 G-box factor 14-3-3 f
THF1 GeneProduct :LOC_Os07g37250 Inositol phosphatase
OsAK GeneProduct :LOC_Os02g41590 Adenosine kinase
BADH2 GeneProduct :LOC_Os08g32870 SCENTED KERNEL 2 (fragrance) betaine-aldehyde dehydrogenase 2
GPT1 GeneProduct :LOC_Os08g08840
BEI GeneProduct :LOC_Os06g51084 expression diminished during grain filling at high temperatures
PHD zf GeneProduct :LOC_Os03g04980
Male sterility protein GeneProduct :LOC_Os05g43040
EF-1-g3 GeneProduct :LOC_Os06g37440 eEF-1B gamma 3
LOC_Os08g04580 GeneProduct :LOC_Os08g04580 Thioredoxin
AOPBP-L GeneProduct :LOC_Os07g48570
CRL1 GeneProduct :LOC_Os03g05510
bZIP GeneProduct :LOC_Os11g06170
CKX2/ Gn1a GeneProduct :LOC_Os01g10110 Cytokinin oxidase/dehydrogenase 2
EIL1 GeneProduct :LOC_Os03g20780
PHD Zn-finger GeneProduct :LOC_Os11g12650
AHOX GeneProduct :LOC_Os10g39030 Associated with HOX family protein, expressed (UniProt Q8LN25)- Assigned as AHOX by Nemeth D and Hanumappa M (08/19/2010)
Smt1-1 GeneProduct :LOC_Os07g10600 Cycloartenol-C24-methyltransferase
SBEIIb GeneProduct :LOC_Os02g32660 expression diminished during grain filling at high temperatures
Acyl carrier GeneProduct :LOC_Os07g12150
Fibrillin GeneProduct :LOC_Os09g04790
OsLKR GeneProduct :LOC_Os02g54254
NAC075 GeneProduct :LOC_Os01g09550
VDAC5 GeneProduct :LOC_Os03g10510
LTPL109 GeneProduct :LOC_Os07g37385 Extensin_2
NAS1 GeneProduct :LOC_Os03g19427 NA synthase gene 1
SCP40 GeneProduct :LOC_Os07g46350 Serine carboxypesidase
BTB-TAZ GeneProduct :LOC_Os01g66890
HRGP GeneProduct :LOC_Os03g13560 Hydroxyproline-rich glycoprotein family protein-UniPret ID
YSL2 GeneProduct :LOC_Os02g43370 yellow stripe 1-like
RALF24 GeneProduct :LOC_Os11g26340 Rapid ALkalinization Factor
DUF584 GeneProduct :LOC_Os05g45450
SuSy5 GeneProduct :LOC_Os02g58480 Sucrose synthase 5
IDEF1 GeneProduct :LOC_Os08g01090 IDE-binding factor 2
PSRR-L GeneProduct :LOC_Os07g25710 Phosphate starvation response regulator
FBL60 GeneProduct :LOC_Os12g33230 Leucine rich repeat
CYP450 GeneProduct :LOC_Os09g10340
Integrase GeneProduct :LOC_Os11g11694
MADS1 GeneProduct :LOC_Os03g11614 Also called LHS1
Hydrolase GeneProduct :LOC_Os02g19650 Iron/ascorbate oxidoreductases
Phragmoplast kinase GeneProduct :LOC_Os04g28260
WRKY 55 GeneProduct :LOC_Os03g20550
Bam 2 GeneProduct :LOC_Os07g35940
CycA1-1 GeneProduct :LOC_Os01g13260
Retrotransposon GeneProduct :LOC_Os12g24050 Sulfotransferase
beta-fructofuranosidase GeneProduct :LOC_Os03g20020 Neutral/alkaline invertase 1 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)
FBK21 GeneProduct :LOC_Os10g21930 F-box domain and kelch repeat containing protein
MADS56 GeneProduct :LOC_Os10g39130
HSP70 GeneProduct :LOC_Os12g14070
PP2A2 GeneProduct :LOC_Os03g59060
SUT3 GeneProduct :LOC_Os10g26470
SSIVb GeneProduct :LOC_Os05g45720
taxane 10-beta-hydroxylase GeneProduct :LOC_Os07g33480 Glutamate synthase cytochrome P450 domain containing protein
ENOD93-1 GeneProduct :LOC_Os06g05010
EF-1-d1 GeneProduct :LOC_Os07g42300 EF-1B beta 1, EF-1-beta
DPE2 GeneProduct :LOC_Os07g46790 Also called ALK
ERG3 GeneProduct :LOC_Os04g44870 RPP16
SIP2 GeneProduct :LOC_Os10g28350 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1 Ethylene induced
Gal1 GeneProduct :LOC_Os10g35110
SGT1 GeneProduct :LOC_Os01g43540 Responds to salicylic acid in chemically induced biotic response
Mald1-AP GeneProduct :LOC_Os01g56470
GlyH GeneProduct :LOC_Os11g27400 Chitinase
VP1 GeneProduct :LOC_Os01g68370 Interaction with Wsi18 and Lea3 by orthology to H vulgare ABA-related Seed dormancy Interaction with Wsi18 and Lea3 by orthology to H vulgare
RCD1-L GeneProduct :LOC_Os04g52340 Also given LOC_Os07g37790 and LOC_Os03g57130
IAA9 GeneProduct :LOC_Os02g56120
vATP synthase C GeneProduct :LOC_Os05g51530
GPT2-3 GeneProduct :LOC_Os07g33910
OsPRP1 GeneProduct :LOC_Os10g05970 Proline rich protein
Amy2A GeneProduct :LOC_Os06g49970 ABA-repressible and GA-inducible
SNAC2 GeneProduct :LOC_Os01g66120 ABA-related
BT1-2 GeneProduct :LOC_Os02g10800
Plasma membrane ATPase GeneProduct :LOC_Os04g56160
IRO2 GeneProduct :LOC_Os01g72370 basic/helix-loop-helix 56
ATP synthetase a GeneProduct :LOC_Os02g54624
SPP2 GeneProduct :LOC_Os02g05030 sucrose-phosphatase 2
MADS 8 GeneProduct :LOC_Os09g32948 Also called MADS 24
SUS2 GeneProduct :LOC_Os06g09450 Sucrose synthase 2
Ubi GeneProduct :LOC_Os09g31031
MADS17 GeneProduct :LOC_Os04g49150 Also called NMADS3 and RMADS213
C3H1 GeneProduct :LOC_Os01g07930 Zinc finger CCCH domain-containing protein Glutaredoxin-related
APL2 GeneProduct :LOC_Os01g44220 ADP-glucose Pyrophosphorylase large subunit 2, binding only happens with APS2b SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF expression diminished during grain filling at high temperatures
Mitrochondrial carrier GeneProduct :LOC_Os03g11510
PGI-b GeneProduct :LOC_Os06g14510
MADS 22 GeneProduct :LOC_Os02g52340 Also called RMD1
GluC GeneProduct :LOC_Os02g15090
ISA1 GeneProduct :LOC_Os08g40930 expression diminished during grain filling at high temperatures
E3-Ubi Ligase GeneProduct :LOC_Os05g47780
DUF151 GeneProduct :LOC_Os01g50622
PHOH GeneProduct :LOC_Os01g63270 Also called ALK
SUS3 GeneProduct :LOC_Os07g42490 Sucrose synthase 3
Ring ZF GeneProduct :LOC_Os04g48050
APS2a GeneProduct :LOC_Os08g25734 Also called AGPS2, ADP-glucose Pyrophosphorylase small subunit 2; SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF has two different transcripts= a:in leaf, b:in endosperm; binding with APL2 and Down regulation by RISBZ1 only happens with APS2b, binding with APL1 only happens with APS2a expression diminished during grain filling at high temperatures
Vin1 GeneProduct :LOC_Os04g45290
CIN4 GeneProduct :LOC_Os01g73580
RB GeneProduct :LOC_Os01g39580 seed coat color, endosperm color
NAC4 GeneProduct :LOC_Os01g60020
MADS 15 GeneProduct :LOC_Os07g01820 Also called RAP1A
ISA3 GeneProduct :LOC_Os09g29404
phosphomannomutase GeneProduct :LOC_Os06g28194 Soluble epoxide hydrolase
CIN7 GeneProduct :LOC_Os09g08072
DAD1 GeneProduct :LOC_Os04g32550 Defender against cell death 1
double-stranded beta-helix domain GeneProduct :LOC_Os11g06370
MADS 16 GeneProduct :LOC_Os06g49840
Bam 3 GeneProduct :LOC_Os07g35880
IDI4 GeneProduct :LOC_Os09g28050 asparate aminotransferase
UGP2 GeneProduct :LOC_Os02g02560
RPBF GeneProduct :LOC_Os02g15350 Functionaly redundant and compensatory expression between RISBZI and RPBF except for OsLKR/SDH double KD mutant (KD-RISBZ1/KD-RPBF) caused most expression change
SAL1 GeneProduct :LOC_Os06g43590
Amy3D GeneProduct :LOC_Os08g36910
PPR bZIP GeneProduct :LOC_Os05g40320 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)
TyrK GeneProduct :LOC_Os11g15340 SAM dependent carboxyl methyltransferase
LOC_Os06g14190 GeneProduct :LOC_Os06g14190
AP-1gamma-1 GeneProduct :LOC_Os06g07090
APS1 GeneProduct :LOC_Os09g12660 ADP-glucose Pyrophosphorylase small subunit 1  expression diminished during grain filling at high temperatures
GF14b GeneProduct :LOC_Os04g38870
Amy1A GeneProduct :LOC_Os02g52710
RACK1A GeneProduct :LOC_Os01g49290 Also called GPB-LR/ RWD
APT1 GeneProduct :LOC_Os12g39860 Adenine phosphoribosyltransferase 1
Bam 1 GeneProduct :LOC_Os10g41550
HOX6 GeneProduct :LOC_Os09g35910 Cooper et al. 2003 called this leucine zipper and misnamed HOX 22 as HOX 6 (22834)
TLR31 GeneProduct :LOC_Os02g53400 Translational repressor MPT5/PUF4
PHOL GeneProduct :LOC_Os03g55090
LOC_Os10g30450 GeneProduct :LOC_Os10g30450 Unknown-UniProt ID
APL3 GeneProduct :LOC_Os03g52460
Sci2 GeneProduct :LOC_Os01g42860
psbC GeneProduct :LOC_Os02g24632
beta-1,3-Glucanase GeneProduct :LOC_Os03g25790
Isocitrate lyase GeneProduct :LOC_Os07g34520
MADS 57 GeneProduct :LOC_Os02g49840
LOC_Os05g06330 GeneProduct :LOC_Os05g06330
PUP2 GeneProduct :LOC_Os06g46740
Oryzain gamma Protease GeneProduct :LOC_Os09g27030
EF-1-g GeneProduct :LOC_Os02g12800 eEF-1G
RISBZ1 GeneProduct :LOC_Os07g08420 Functionaly redundant and compensatory expression between RISBZI and RPBF. Double Knock-Down mutant (KD-RISBZ1/KD-RPBF) caused most expression change in OsLKR/SDH
bip110 GeneProduct :LOC_Os06g08530 Putative ubiquitin-specific protease 23, BRI1-KD interacting protein 110
SUT4 GeneProduct :LOC_Os02g58080
Flavin containing monooxygenase 3-like GeneProduct :LOC_Os09g37620 Serine/threonine protein kinase
Ghd7 GeneProduct :LOC_Os07g15770 yield potential
Wsi18 GeneProduct :LOC_Os01g50910 Interaction with TRAB1 and VP1 by orthology to H vulgare ABA and GA induced water stress + cold stress member of the group 3 Lea family Wsi18 promoter is active in the whole grain
PGI-a GeneProduct :LOC_Os09g29070
Wx1 GeneProduct :LOC_Os06g04200 30% less pre-mRNA in du1 mutant line Granule-bound starch synthase expression diminished during grain filling at high temperatures
GPT-A GeneProduct :LOC_Os05g07670 Assigned as GPT-A by Nemeth D and Hanumappa M (10/21/2010)
MADS 14 GeneProduct :LOC_Os03g54160 Also called AGL10, RAP1B
ABI5 GeneProduct :LOC_Os01g64000
AOXDH GeneProduct :LOC_Os03g31550
Serine protease GeneProduct :LOC_Os04g45910 Os04g0542900,
VP2-like GeneProduct :LOC_Os03g05750
RAR1 GeneProduct :LOC_Os02g33180
SUT1 GeneProduct :LOC_Os03g07480
Flavin-containing monooxygenase GeneProduct :LOC_Os01g15540
CSN5 GeneProduct :LOC_Os04g56070
PROLM 24 GeneProduct :LOC_Os06g31070 16 kDa Prolamin
Importin alpha-1a GeneProduct :LOC_Os01g14950 NLS RECEPTOR
APRL3 GeneProduct :LOC_Os02g51850 Disulfide Isomerase
RAC GeneProduct :LOC_Os01g12900
LOC_Os02g08530 GeneProduct :LOC_Os02g08530 Protein Kinase-UniProt ID
Anthranilate Phosphoribosyltransferase GeneProduct :LOC_Os03g03450
Amy3B/Amy3C GeneProduct :LOC_Os09g28420
DU1 GeneProduct :LOC_Os10g35550 dull endosperm-1
Sci2 GeneProduct :LOC_Os01g42860
Centromere protein GeneProduct :LOC_Os03g20580
PIP5K GeneProduct :LOC_Os02g57660 Putative phosphatidylinositol-4-phosphate 5-kinase
REB GeneProduct :LOC_Os03g58250 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)
Lea3 GeneProduct :LOC_Os05g46480 Interaction with TRAB1 and VP1 by orthology to H vulgare ABA related
DPK4 GeneProduct :LOC_Os06g45300 Ser/thr/tyr kinase
LOC_Os10g40260 GeneProduct :LOC_Os10g40260
Luc7-like 2 GeneProduct :LOC_Os03g62640 Sarcoplasmic reticulum
Jasmonate-induced protein GeneProduct :LOC_Os12g09700 Histone H3 (Lys9) methyltransferase
OsEM GeneProduct :LOC_Os05g28210
SBEIIa GeneProduct :LOC_Os04g33460 expression diminished during grain filling at high temperatures
Ankyrin-like protein GeneProduct :LOC_Os09g17329 Iron transporter
Vin 2 GeneProduct :LOC_Os02g01590
Bam 10 GeneProduct :LOC_Os03g22790
ALDP GeneProduct :LOC_Os11g07020 Aldolase
GluA-1 GeneProduct :LOC_Os01g55690
RCAA1 GeneProduct :LOC_Os11g47970 RuBisCO activase large isoform
PPDKB GeneProduct :LOC_Os05g33570 CPDK1, PPDKB
PSI-D GeneProduct :LOC_Os08g44680
SSIVa GeneProduct :LOC_Os01g52250 Also called ALK
LOC_Os03g03860 GeneProduct :LOC_Os03g03860 Unknown-UniProt ID
PBZ1 GeneProduct :LOC_Os12g36880
SSA2 GeneProduct :LOC_Os03g55730 10 kDa prolamin precursor
LOC_Os03g43910 GeneProduct :LOC_Os03g43910
MADS5 GeneProduct :LOC_Os06g06750
GLN1-1 GeneProduct :LOC_Os02g50240 Glutamine synthetase cytosolic isozyme 1-1, also called RGS28 and GS1;1
MPK5 GeneProduct :LOC_Os03g17700 UniProt:MPK3, BIMK1, MAP3, MAPK2, MPK5
HDS1 GeneProduct :LOC_Os02g39160 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1
SCR-like GeneProduct :LOC_Os02g45760 Scarecrow transcriptional regulator-like protein
CYP450 GeneProduct :LOC_Os10g08474 AP2 transcription factor
TRAB1 GeneProduct :LOC_Os08g36790 Interaction with Wsi18 and Lea3 by orthology to H vulgare bZIP transcription factor TRAB1, ABA RESPONSIVE ELEMENT 1=ABA1
YSL15 GeneProduct :LOC_Os02g43410 YELLOW STRIPE LIKE 15
ferroportin1 GeneProduct :LOC_Os06g36450
LOC_Os03g55130 GeneProduct :LOC_Os03g55130
Bam 9 GeneProduct :LOC_Os02g03690
Photosystem I RC subunit GeneProduct :LOC_Os07g05480
SSI GeneProduct :LOC_Os06g06560
EXPB2 GeneProduct :LOC_Os10g40710
Stress-related protein GeneProduct :LOC_Os07g47510
Bam 8 GeneProduct :LOC_Os01g13550
Phospholipase C GeneProduct :LOC_Os07g49330
SUT5 GeneProduct :LOC_Os02g36700
INV3 GeneProduct :LOC_Os02g32730 Neutral/alkaline invertase 3 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)
Delta-COP GeneProduct :LOC_Os01g61710 Delta coatamer
SSII-2 GeneProduct :LOC_Os02g51070 Also called ALK
Terpene cyclases GeneProduct :LOC_Os04g27190
MCM2 GeneProduct :LOC_Os11g29380
Rab21 GeneProduct :LOC_Os11g26790 ABA related water stress + cold stress
CML18 GeneProduct :LOC_Os05g13580
GF14c GeneProduct :LOC_Os08g33370
UGP1 GeneProduct :LOC_Os09g38030
FDH GeneProduct :LOC_Os02g57040 Alcohol dehydrogenase class 3; Also called FALDH, GSH-FDH (Glutathione-dependent formaldehyde dehydrogenase)
LOC_Os05g50190 GeneProduct :LOC_Os05g50190 Protein Kinase-UniProt ID
LOC_Os04g41910 GeneProduct :LOC_Os04g41910
RIR 1b GeneProduct :LOC_Os05g48260
CPL1 GeneProduct :LOC_Os07g10690 Seed Shattering
FBO10 GeneProduct :LOC_Os11g34460 Adagio-like protein 3 Cytochrome P450
OsCCP GeneProduct :LOC_Os12g08760
JA cmtr GeneProduct :LOC_Os06g22440 Putative S-adenosyl-L-methionine Subtilisin N-terminal Region
ISA2 GeneProduct :LOC_Os05g32710
Bam 6 GeneProduct :LOC_Os09g39570
PROLM28 GeneProduct :LOC_Os12g16890 Prolamin precursor, protein also called PPROL 17
Pumilio GeneProduct :LOC_Os12g31000 Leucine rich repeat
IRT1 GeneProduct :LOC_Os03g46470
Oligopeptide transporter 3 GeneProduct :LOC_Os03g54000 Isp4-like
MADS-box IL GeneProduct :LOC_Os02g54080
ATP synthase GeneProduct :LOC_Os03g17070
GluB-1A GeneProduct :LOC_Os02g15169 UniProt ID: P14323
MLA10 GeneProduct :LOC_Os11g16470 Ankyrin repeat
RPK-TMK1 precursor GeneProduct :LOC_Os04g58910 receptor protein kinase TMK1 precursor
MADS 2 GeneProduct :LOC_Os01g66030
LOC_Os12g37570 GeneProduct :LOC_Os12g37570 Protein Kinase-UniProt ID
DIP1 GeneProduct :LOC_Os05g34070
EBP89 GeneProduct :LOC_Os03g08460 Also called EREBP1
SUT2 GeneProduct :LOC_Os12g44380
CycB1;1 GeneProduct :LOC_Os01g59120 Seed Shattering
SPP1 GeneProduct :LOC_Os01g27880 sucrose-phosphatase 1
S-REP GeneProduct :LOC_Os04g47990
bhlh113 GeneProduct :LOC_Os10g40740 basic/helix-loop-helix 113
APL1 GeneProduct :LOC_Os05g50380 ADP-glucose Pyrophosphorylase large subunit 1
CTR1-like GeneProduct :LOC_Os09g39320 Multitransmembrane protein
DREB1B GeneProduct :LOC_Os09g35010
RUBQ1 GeneProduct :LOC_Os02g06640 Also called Polyubiquitin 6 Also given LOC_Os05g42424 which is not complete
NADPH G-3-P dh GeneProduct :LOC_Os08g34210
Sdr4 GeneProduct :LOC_Os07g39700
Ring Finger GeneProduct :LOC_Os01g01390
SSIIc GeneProduct :LOC_Os10g30156 Also called ALK
LOC_Os04g57020 GeneProduct :LOC_Os04g57020
PSII-OEP33 GeneProduct :LOC_Os01g31690 No symbol in gramene so OEP33 was assigned. 33kDa oxygen evolving protein of photosystem II
LOC_Os04g53350 GeneProduct :LOC_Os04g53350 Cooper 31122 ID
CRINKLY4 GeneProduct :LOC_Os08g28710
RAG-1 GeneProduct :LOC_Os09g16260 RISBZ1 + RPBF activated the RAG-1 promoter greater than RPBF alone, though RISBZ1 did not independently affect promoter activity
CR4 GeneProduct :LOC_Os03g43670 homology with Crinkly4
SSA1 GeneProduct :LOC_Os05g41970 26 kDa alpha globulin
TATC GeneProduct :LOC_Os01g31680
DPE1 GeneProduct :LOC_Os07g43390
LOC_Os02g53890 GeneProduct :LOC_Os02g53890


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