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).fcaIn Cooper et al. 2003 protein sequence provided matches HOX 22, however it was named HOX6 (AF145730)e3be3baa5e3ba18Helix-loop-helix TF e3bAlso called MADS 28e3bInvolved in grain fillinga10e3bGlobulin 2e3ba55b192-keto-3-deoxy-6-phosphogluconate aldolaseff9e3bJacalinff9e3be3bBeta-expansin-4b19c5ce3bsucrose-phosphate synthase-Oncidium spp= named after table III on Yamakawa et al. (2007)
fc4d54e3bfc4c5cthiol-disulphide oxidoreductase DCCe3be3be3be3bProliferating cell nuclear antigen
expressed strongly in the shoot apical meristeme3ba18f34SGNH_plant_lipaseff9e3bcatalytic C-terminal domain containing proteinff9Also called ALKb09ff5ff9ABA-inducible & GA-repressible
WRKY 51 by itself also represses activation of Amy2A by GAMYBcc3e18transcripts of both OsRad6 and OsSgt1 were found to be strongly expressed in the proliferating tissues such SAMe3ba71e3be3bff9ff9Also called ALKb09ff5Elongation factor 1 beta 2e3be3bCdc2-related protein kinaseff9de6e1ce3be3bc10a10b19e3bb19Amino acid/polyamine transporter ff9e3bbZIP transcription factor domain containing proteine3bUniProt:MAPK2, BIMK1, MAP3, MAPK5, MPK3, MSRMK2e3bInitiation factor 2 subunit family proteinf4fa87ff9ebeaa5Also called ALKff5b09e3bProtein Kinase-UniProt IDe3be3bNeutral/alkaline invertase 2
Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)fc4ff95-Enolpyruvylshikimate-3-phosphate synthase 1e3be78b09bf5fc4Putative protein kinase e3bsucrose-phosphate synthase-Zea mays= named after table III on Yamakawa et al. (2007)
fc4e3bLIM domain-containing protein, putative, expressede3be3bProbable voltage-gated potassium channel subunit betab19G-alpha protein also called GPA1/D1/GA1a553-deoxy-D-arabino heptulosonate-7-phosphate synthase 1 b19nicotianamine aminotransferase f4fABA relatedebeexpression diminished during grain filling at high temperatures
b09f43ff5ea9fc4e3be3bsucrose-phosphate synthase-Saccharum officinarum= named after table III on Yamakawa et al. (2007)
fc4e3bc10a10b19Methylthioadenosine/S-adenosyl homocysteine nucleosidasef4fP35686 e3be3be3bSalt-stress
ABA relatedde9also called MADS 45, AGL6, M79e3bb8e1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2; Also called IDI1 and SIP2Af4fregulates GA induction of Amy2Acc3fd4Needed 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 desiccationd99e3bABA-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 GAMYBcc3fd4Assigned as Complex 1L by Nemeth D and Hanumappa M (10/21/2010)
complex 1 family protein-like (LYR family)b19e3bWIN2, WIP2e3be1cProlamin precursor, also called RP5e3bed7ba3d54Assigned as bHLH-tf by Nemeth D and Hanumappa M (10/21/2010)b19e3bd29e3bexpression diminished during grain filling at high temperatures
b09ff5ea9d0bSucrose synthase 6
fc4bfce3bAmino acid transportersff9Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)e3baa5bf5Na+ dep inorg phosphate cotransporter e3be3b2 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).Type your comment heree3bGTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthasee3bubiquitin carboxyl-terminal hydrolase, family 1, putative, expressede3be3bff9fc4c5ce8fhistone-lysine N-methyltransferaseff9NAD(P)-binding/Rossman folde3brequired for storage product accumulation during seed development
seed-specific protein kinasec69c8ea48Also called RAGe3bETFP adenine nucleotidee3be3bAssigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)fc4fc4sucrose-phosphate synthase-Hordeum vulgare= named after table III on Yamakawa et al. (2007)
fc4ccdNA synthase gene 2 f4fencodes a RING protein with E3 ubiquitin ligase activitya17c4ce3bba3d54fc4Haloacid dehalogenase-like hydrolase family proteinf4f2-oxoglutarate (2OG) - Fe(II) oxygenase ff9Bowman-Birk type bran trypsin inhibitor b19e3b13 kDa Prolamin, also called PPROL 14, PPROL 4A, PPROL 7, PG5a, PROLM 8, PROLM 9, UniProt ID: Q95737c10a10e75c67e8de3bAlso called MFO1e3be3bb19Sucrose synthase 4
fc4e3bbf5IDE-binding factor 2 f4fe8faa5Sucrose synthase 1
fc4e3bfc4Class III peroxidase 61aa5Also called MAF1e3bff9f4ab09e3be3be3bAssigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)fc4expression diminished during grain filling at high temperaturesff5f15e18e3be3bc67e8dTubulin beta-3 chainb19b6df97Also called ZFP60e3bAlso called MDPe3bbf5Deoxymugineic acid synthase1 f4fe8de3be3be3bfd6bbde75c67e8da10seed coat color, endosperm colordfcAlso called HSP81-2bc8b22G-box factor 14-3-3 fe3bInositol phosphatasee3bAdenosine kinase e3bSCENTED KERNEL 2 (fragrance) betaine-aldehyde dehydrogenase 2efcde1dbefc4expression diminished during grain filling at high temperaturesb09f4ae3be3beEF-1B gamma 3e3bThioredoxinff9e3bd54e3bCytokinin oxidase/dehydrogenase 2 a17c4cb6dff9Associated with HOX family protein, expressed (UniProt Q8LN25)- Assigned as AHOX by Nemeth D and Hanumappa M (08/19/2010)e3bCycloartenol-C24-methyltransferasee3bexpression diminished during grain filling at high temperaturesb09ea9f4ae18e3be3ba5ae3be3bExtensin_2
ff9NA synthase gene 1 f4fSerine carboxypesidasee3be3bHydroxyproline-rich glycoprotein family protein-UniPret IDe3byellow stripe 1-like aa5Rapid ALkalinization Factoraa5ff9Sucrose synthase 5
fc4IDE-binding factor 2f4fe8faa5Phosphate starvation response regulator e3bLeucine rich repeat ff9ff9ff9Also called LHS1e3bIron/ascorbate oxidoreductasesff9e3bd54c5cf8bbf5Sulfotransferaseff9Neutral/alkaline invertase 1
Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)fc4F-box domain and kelch repeat containing proteine3be3be3bbc8b22e3bfc4b09ff5ea9Glutamate synthase
cytochrome P450 domain containing proteinff9fb5EF-1B beta 1, EF-1-betae3bAlso called ALKf15RPP16e3b1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1
Ethylene inducede7cff9e3bResponds to salicylic acid in chemically induced biotic responsebc8b70c16b22a71e3be3bChitinaseff9Interaction with Wsi18 and Lea3 by orthology to H vulgare
ABA-related
Seed dormancy
Interaction with Wsi18 and Lea3 by orthology to H vulgaree3be1cb08Also given LOC_Os07g37790 and LOC_Os03g57130b19d54e3bfc4Proline rich proteine3bABA-repressible and GA-induciblecc3fd4ABA-relatedebec17fc4e3bbasic/helix-loop-helix 56 f4fe8faa5e3bsucrose-phosphatase 2
fc4Also called MADS 24e3bSucrose synthase 2
fc4aa5Also called NMADS3 and RMADS213e3bZinc finger CCCH domain-containing protein Glutaredoxin-related e3bADP-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 temperaturesb09e78ea9d0ba10e3bfc4Also called RMD1b3ce3ba10expression diminished during grain filling at high temperatures
b09d0beeee3bff9Also called ALKff5b09Sucrose synthase 3
fc4e3bAlso 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 temperaturesb09e78ea9d0ba10fc4e8dseed coat color, endosperm colordfce8fAlso called RAP1Ae3bb09e18eeeSoluble epoxide hydrolaseff9e8dfc4Defender against cell death 1e3bff9e3bc5casparate aminotransferasef4ffc4Functionaly redundant and compensatory expression between RISBZI and RPBF except for OsLKR/SDH
double KD mutant (KD-RISBZ1/KD-RPBF) caused most expression changec10a10a10fc4Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)e3bSAM dependent carboxyl methyltransferaseff9e3be3bADP-glucose Pyrophosphorylase small subunit 1Â
expression diminished during grain filling at high temperaturese78ea9b09e3be1cfc4Also called GPB-LR/ RWDa55bc8Adenine phosphoribosyltransferase 1f4fc5cCooper et al. 2003 called this leucine zipper and misnamed HOX 22 as HOX 6 (22834)e3bTranslational repressor MPT5/PUF4ff9f15e18Unknown-UniProt IDe3be78b09bbbe3bb19ff9e3be3bebee3beEF-1Ge3bFunctionaly redundant and compensatory expression between RISBZI and RPBF.
Double Knock-Down mutant (KD-RISBZ1/KD-RPBF) caused most expression change in OsLKR/SDHc10a10Putative ubiquitin-specific protease 23, BRI1-KD interacting protein 110e3bfc4Serine/threonine protein kinaseff9yield potentialdcdfd6a17eb4c4cInteraction 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 graina5fba7b08e3bfc430% less pre-mRNA in du1 mutant line
Granule-bound starch synthase
expression diminished during grain filling at high temperaturese3bff5ea9b05d0bAssigned as GPT-A by Nemeth D and Hanumappa M (10/21/2010)fc4Also called AGL10, RAP1Be3be43b08e3bOs04g0542900, e3be3bbc8b70b22fc4ff9c0216 kDa Prolamina10c10NLS RECEPTOR e3bDisulfide Isomerase e3bbc8ed7Protein Kinase-UniProt IDe3be3bfc4dull endosperm-1e78ea9e18d54e3bPutative phosphatidylinositol-4-phosphate 5-kinasee3bSymbol assigned by Nemeth D and Hanumappa M (08/19/2010)e3bInteraction with TRAB1 and VP1 by orthology to H vulgare
ABA relateda5fde9eceebeb08Ser/thr/tyr kinase e3be3bSarcoplasmic reticulum e3bHistone H3 (Lys9) methyltransferaseff9e8fe81b08expression diminished during grain filling at high temperaturesea9f4ab09e18Iron transporterff9fc4c5cAldolase e3bb19c10e3ba10RuBisCO activase large isoforme3bCPDK1, PPDKBe3be3bAlso called ALKb09ff5Unknown-UniProt IDe3bd5410 kDa prolamin precursore3be3be3bGlutamine synthetase cytosolic isozyme 1-1, also called RGS28 and GS1;1e3bUniProt:MPK3, BIMK1, MAP3, MAPK2, MPK5e3b4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1cfee3bScarecrow transcriptional regulator-like proteine3bAP2 transcription factorff9Interaction with Wsi18 and Lea3 by orthology to H vulgare
bZIP transcription factor TRAB1, ABA RESPONSIVE ELEMENT 1=ABA1e3bb08YELLOW STRIPE LIKE 15f4fff9e3bc5ce3be18e3be3bc5ca55fc4Neutral/alkaline invertase 3
Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)fc4Delta coatamer e3bAlso called ALKff5b09ff9c02ABA related
water stress + cold stressa5ff65e3be3be1cfc4Alcohol dehydrogenase class 3; Also called FALDH, GSH-FDH (Glutathione-dependent formaldehyde dehydrogenase)f4fProtein Kinase-UniProt IDe3be3be3bSeed ShatteringedbAdagio-like protein 3
Cytochrome P450ff9Assigned as OsCCP by Nemeth D and Hanumappa M (10/21/2010)
carboxyvinyl-carboxyphosphonate phosphorylmutaseb19Putative S-adenosyl-L-methionine
Subtilisin N-terminal Regionff9b09eeefc4c5cProlamin precursor, protein also called PPROL 17 e3bLeucine rich repeatff9e8fe60Isp4-like e3be3be3bUniProt ID: P14323b19c10a10e3bAnkyrin repeatff9receptor protein kinase TMK1 precursore3be3bProtein Kinase-UniProt IDe3be3bAlso called EREBP1b6db05fc4Seed Shatteringad9sucrose-phosphatase 1
fc4e3bbasic/helix-loop-helix 113e3bADP-glucose Pyrophosphorylase large subunit 1 b09e78ea9Multitransmembrane proteinff9aa5Also called Polyubiquitin 6
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