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Word Map for Organism Oryza sativa Japonica Group
- Oryza sativa Japonica Group
- nipponbare
- panicle
- amylose
- rufipogon
- endosperm
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landraces
- planthopper
- tiller
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koshihikari
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marker-assisted
- amylopectin
- ssiia
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spikelet
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map-based
- taipei
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near-isogenic
- magnaporthe
- nivara
- shattering
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waxy
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kasalath
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sake
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chalkiness
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booting
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zhonghua
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basmati
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indica-japonica
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glutinous
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photoperiod-sensitive
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fine-mapping
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granule-bound
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grain-filling
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yield-related
TaxTree of Organism Oryza sativa Japonica Group
Condensed Tree View
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EC NUMBER 
COMMENTARY 
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transferred to EC 1.14.14.107
transferred to EC 1.14.14.151
preliminary BRENDA-supplied EC number
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
(5R)-carbapenem carboxylate biosynthesis
catecholamine biosynthesis
cyanate degradation
degradation of aromatic, nitrogen containing compounds
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diterpene phytoalexins precursors biosynthesis
folate polyglutamylation
methylaspartate cycle
octane oxidation
suberin monomers biosynthesis
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SwissProt
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700777, 726190, 743467, 746244, 741522, 743819, 741530, 743806, 742058, 743628, 742051, 746266, 746218, 744147, 744525, 744895, 746144, 744499, 746089, 746311, 746097, 746126, 755868, 758063, 757481, 757363, 758040, 757963, 758039, 756811, 738913, 738818, 738614, 739330, 743479, 738765, 749680, 751641, 752264, 756836, 758019, 748927, 706253, 747870, 746981, 746596, 748913, 749018, 749378, 744876, 749033, 749318, 747784, 748926, 747199, 748774, 746112, 746114
Q0JA75, Q0J8A4, Q7XKF3, Q8W3D9, U5LY03, Q652L6, Q65XA0, Q10N21, Q9FE01, Q76I22, Q10RP4, Q9SDJ2, Q6YV88, A3A871, Q851G2, Q5Z5R4, Q7XB43, Q84NP3, Q6ZD89, B9EZV5, Q5KQI6, Q7XXN4, Q10PV5, Q2QXY9, Q2RAP8, Q84ZN6, Q0DWQ1, A0A0P0X1V6, A0A0P0XHN6, Q1WM16, Q10M74, Q2QPW1, Q84JH5, Q941T9, Q6ZJ97, Q7XEJ4, Q75WV3, B9F813, B9FDB8, Q9SSX0, Q8H4V1, Q0JC10, Q0JA82, Q2QQJ5, Q6Z5J6, A4KAG8, Q2R2A6, C7AU21, Q6H5C7, Q9FTR6, Q53LQ0, Q6Z4G3, Q8H8T0, H2KWF1, Q851K9, Q851M0
Uniprot
amino acid position 126 is Arg in cultivar Norin 1 and Gln in cultivar Sasanishiki
SwissProt
cDNA clones of CYP75B3 are isolated from the white rice, Iimi (IM), black rice, Heugnam (HN) and Heugjinju (HJJ), and red rice, Jeogjinju (JJJ) and Hongjinju (HoJJ). Three cDNA clones of CYP75B3 encoded proteins of 526 amino acids (CYP75B3-IM, CYP75B3-HN, and CYP75B3-JJJ). Amino acid sequence comparison reveals that CYP75B3-IM and CYP75B3-JJJ are identical to the registered sequence in UNIPROT database, but one amino acid is substituted in the CYP75B3-HN sequence at position 27. An additional substitution is observed in the CYP75B4-HJJ sequence at position 258. His27 of CYP75B3-HN is located at the N-terminal membrane anchor region; however, the other cytochrome P450-specific conserved regions, such as the oxygen binding pocket, the ExxR motif, and the heme binding domain, are identical among all of the isolated genes, while most of the substrate recognition sites are different between CYP75B3s. The Thr504 of each CYP75B3, known as functional determinant for the specific enzyme activity, is conserved
SwissProt
cDNA clones of CYP75B4 are isolated from the white rice, Iimi (IM), black rice, Heugnam (HN) and Heugjinju (HJJ), and red rice, Jeogjinju (JJJ) and Hongjinju (HoJJ). Five cDNA clones of CYP75B4-encoded proteins of 535 amino acids (CYP75B4-IM, CYP75B4-HN, CYP75B4-HJJ, CYP75B4-JJJ, and CYP75B4-HoJJ). Amino acid sequence comparison reveal that CYP75B4-IM is identical to the registered sequence in UNIPROT, but an amino acid substitution at position 351 is shared by CYP75B4-HN and CYP75B4-HJJ from black rice and another substitution at positions seven is shared by CYP75B4-JJJ and CYP75B4-HoJJ from red rice. An additional substitution is observed in the CYP75B4-HJJ sequence at position 258. Val7 of CYP75B4-JJJ and CYP75B4-HoJJ are located at the N-terminal membrane anchor region; however, the other cytochrome P450-specific conserved regions, such as the oxygen binding pocket, the ExxR motif, and the heme binding domain, are identical among all of the isolated genes, while most of the substrate recognition sites are different between CYP75B4s. The Leu512 of each CYP75B4, known as functional determinant for the specific enzyme activity, is conserved. The other substitutions, His258 of CYP75B4-HJJ and Gln351 of CYP75B4-HN and CYP75B4-HJJ, are located out of the functional regions
SwissProt
cv. Nipponbare
UniProt
cZOGT1; three isozymes cZOGT1, cZOGT2, and cZOGT3, six nuclear genes cZOG
UniProt
cZOGT2; three isozymes cZOGT1, cZOGT2, and cZOGT3, six nuclear genes cZOG
UniProt
cZOGT3; three isozymes cZOGT1, cZOGT2, and cZOGT3, six nuclear genes cZOG
UniProt
OsGS1;1; var. indica, drought-sensitive IR-64 cultivar and drought-tolerant Khitish cultivar, gene OsGS1;1
SwissProt
SPL29; cvs. Guangzhan63s, 10N056, Yuehui9113, and Zhonghua 11
UniProt
subspecies Oryza sativa japonica, strains Sasanishiki, Norin 1, and Surjamkhi
SwissProt
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
PGL, encoding chlorophyllide a oxygenase 1, is mainly expressed in the chlorenchyma
highest expression in the leaf, followed by the pod and the panicle
OsUAM1 and OsUAM2 are expressed ubiquitously throughout plant development, but OsUAM3 is expressed primarily in reproductive tissue, particularly at the pollen cell wall formation developmental stage
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additional information
the enzyme is specifically expressed in the tapetum of anthers
OsGLN1,1, under nitrogen-limited condition
OsGLN1,2, under nitrogen-sufficient condition
OsGLN1,1, under nitrogen-limited condition
OsGLN1,2, under nitrogen-sufficient condition
isozyme OsPSS-1 gene is expressed predominantly in elongating cells
grain tocotrienol and HGGT levels increase in the early stage and then reach a plateau
Q6Z2T6, Q2QXY1, Q2RAP0, B9FLJ1, Q0JKD0, Q69RJ0, Q65XA0, Q53WJ1, Q9SDJ2, Q68YV7, Q68YV9, Q6GZ42, Q10RT5, Q84NP3, Q0DF89, Q6ZFJ3, Q6ZD89, Q7XXN4, Q10PV5, B7F7B9, Q0JGK4, Q53JI9, Q67WN8, Q6ZHZ1, Q0DWQ1, A0A0P0X1V6, A0A0P0XHN6, Q10M74, Q2QPW1, Q6Z9A3, Q84JH5, Q941T9, Q6ZJ97, Q0JR55, Q0DWY3, Q2QWU2, Q5VP94, Q6YV04, Q0JC10, Q6F6A2, Q2QQJ5, Q6Z5J6, Q6BDZ9, A4KAG8, Q948T6, P14656
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746502, 745635, 726482, 743294, 742734, 755243, 746218, 676582, 736578, 746126, 728513, 757484, 757363, 758040, 720763, 756811, 738913, 738614, 739330, 738765, 739446, 741174, 711072, 706253, 694574, 694713, 728501, 746981, 746596, 730617, 748914, 728470
expressed at high levels in developing leaves, expression decreases dramatically in fully mature leaves
expression is relatively constant throughout leaf development
FC1 is expressed slightly more at the seedling stage than at the heading stage
highest expression among the tissues tested. In plants carrying the Zebra leaf mutation, yellow and green striped leaves appear at the seedling stage and gradually turn pale green towards the end of the tillering stage
low expression level at blade sheath, high expression level at blade ear
OsAS2 mRNA is abundant in leaf blades and sheathes of rice
highest expression in the leaf, followed by the pod and the panicle
Q10PV5, B7F7B9, Q0JGK4, Q53JI9, Q67WN8, Q6ZHZ1, Q6Z9A3, Q84JH5, Q941T9, Q0JR55, Q9FWQ2, Q6H5L4, B9FDB8, A0A0F7QZZ2, Q8LNZ3, P14654, P14656, Q4W8D0
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757362, 758040, 720763, 739330, 739446, 679760, 751680, 756836, 746968, 749149, 748914, 728465, 728470
FC1 is expressed slightly more at the seedling stage than at the heading stage
gene OsEGL1 is expressed in seedling, and young and adult plant roots
NADH-GOGAT is primarily located in plastids of non-photosynthetic tissues such as roots
OsAS2 mRNA is detectable in the roots, its content decreases when NH+4 is supplied
OscZOG1 is highly expressed in primary root meristem and lateral root primordia in rice
OsGLN1,1 is expressed in epidermis and exodermis under nitrogen-limited condition. Within the central cylinder of the elongating zone the enzyme is induced by ammonium
OsGLN1,2 is expressed in epidermis and exodermis under nitrogen-sufficient condition. Within the central cylinder of the elongating zone the enzyme is induced by ammonium
OsGS1;2 gene is mainly expressed in surface cells of roots
root surface cell-specific expression of OsAS1 gene. OsAS1 is mainly expressed in the roots, with in situ hybridization showing that the corresponding mRNA is specifically accumulated in the three cell layers of the root surface (epidermis, exodermis and sclerenchyma) in an NH4+-dependent manner
Q2QXY1, Q2RAP0, Q76I22, Q2QXY9, Q2RAP8, B7F7B9, Q0JGK4, Q53JI9, Q67WN8, Q6ZHZ1, D6QSX9, Q2QWU2, Q5VP94, Q6YV04
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expressed predominantly in the developing seeds of black rice and not in those of white and red rice
predominantly expressed in developing seeds during active starch synthesis
U5LY03, Q6Z2T6, Q76I22, Q53WJ1, Q9SDJ2, Q851G2, B9EZV5, Q0JB48, Q7XU02, Q7XU03, Q7XSZ0, Q6ZJ97, Q0JR55, Q0DWY3, Q6H5L4, Q5UAW3, Q2QWU2, Q5VP94, Q6YV04, Q8LNZ3, Q851K9, P14656, Q10MX3, Q43011
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746244, 746502, 743320, 743426, 755243, 746218, 746144, 758063, 723476, 736599, 738765, 739446, 741174, 751680, 709698, 711072, 749149, 748914, 746112, 728470, 709317, 746041
highest expression in aerial part of 2-week-old seedlings
FC1 is expressed slightly more at the seedling stage than at the heading stage. At the heading stage, a strong FC1 expression level in the first internode
additional information
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(R)-beta-tyrosine occurs in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Dry rice seeds from plants that have not been elicited with jasmonic acid also contain significant amounts of beta-tyrosine. When rice seedlings are grown hydroponically, beta-tyrosine is secreted into the medium
additional information
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BC12 is mainly expressed in tissues undergoing cell division and secondary wall thickening
additional information
cultivar/tissue specific expression of r9-LOX1, the expression is generally much higher in active bran/seed than in stabilized bran, mature seeds, and regenerated plants
additional information
Q10RT5
enzyme expression analysis in different tissues of rice
additional information
enzyme expression in relation to N levels in roots and shoots, overview
additional information
expressed in all tested tissues and organs, with the highest expression in the leaf, followed by the pod and the panicle. Lowest expression in stem and the root
additional information
gene OsCRD1 is mainly expressed in green tissues, including stem, leaf, tassel and sheath, but not in root
additional information
increase in OsTPP7 expression between 2 and 4 days of growth in the dark under submergence, elevated expression under submergence and an absence of OsTPP7 expression in leaves. Anaerobic germination is tolerated through the presence of a functional OsTPP7 gene
additional information
isozyme OsAS1 mRNA is the major species in rice roots when the seedlings are hydroponically grown for 18 d after germination with water
additional information
KAO is broadly expressed in many organs and tissues
additional information
low constitutive expression of Osr9-LOX1 in rice leaves, stems, and spikelets, but high constitutive expression in roots, expression analysis
additional information
main expression in sclerenchyma cell of secondary cell wall and vascular bundle region. Panicle, at the heading stage, show strong FC1 expression level
additional information
mRNA and protein contents of GS isoforms, overview
additional information
OsAS1 mRNA is the major species in rice roots when the seedlings are hydroponically grown for 18 d after germination with water
additional information
OscZOG1 is preferentially expressed in shoot and root meristematic tissues and nascent organs
additional information
OsUAM3 coexpression networks include pectin catabolic enzymes. Co-expression network in silico analysis, quantitative RT-PCR analysis of OsUAM isozymes gene expression in various organs at different developmental stages, overview
additional information
OsVTC1-8 transcript level is low in both leaves and roots
additional information
quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses of wild-type plants reveals that OsPSS-1 is expressed in various organs, including roots, culms, and leaves, with the highest expression in panicles
additional information
the enzyme is ubiquitously distributed in the plant. Relatively higher expression of OsMKK4/SMG1 is detected in younger organs than in older ones
additional information
tissue specificity and diurnal change in gene expression of the sucrose phosphate synthase gene family, overview. Isozyme comparison: gene SPS1 is preferentially expressed in source tissues, whereas genes SPS2, SPS6, and SPS8 are expressed equally in source and sink tissues, mRNA levels of SPS1, SPS8, and SPS11 are considerably higher in seeds than in shoots and roots
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
NADH-GOGAT is primarily located in plastids of non-photosynthetic tissues such as roots
additional information
OsBGlu16-GFP fusion protein is localized to the cell wall, when expressed in tobacco leaf epithelial cells
Q6Z2T6, B9FLJ1, Q0JKD0, Q9SDJ2, Q851G2, Q5KQI6, Q6Z1Y6, Q0DWQ1, Q10M74, Q2QPW1, P15280, Q7XEJ4, Q8H4V1, Q0JA82, A4KAG8, Q0DIV0, Q69TB1, Q2R2A6, Q851K9
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746502, 726482, 746218, 746144, 746439, 756156, 756811, 738614, 737807, 749680, 748927, 747870, 746981, 716025, 749378, 746112
contains a relatively high proportion of the phosphorylated CPD photolyase
the chloroplast localization signal of OsCAO1 likely exists in the N-terminus
the enzyme contains a N-terminal transit peptide sequence
the enzyme contains an N-terminal transit peptide sequence
the first 58 residues of OsKSL2 function as a putative chloroplast transit peptide
Q10RT5
integral enzyme, the enzyme contains two putative transit peptides at its N-terminus, which are essential for its functionality, suggesting that targeting of the enzyme to the chloroplast is likely mediated by a putative bipartite transit peptide. Once the precursors of luminal proteins reach the stroma, the first transit peptide for the chloroplast envelop is cleaved off by the stroma processing proteases, and then the intermediate precursor lacking the first transit peptide is translocated into the thylakoid lumen through the second transit peptide
Q0J8A4, Q652L6, Q65XA0, Q9FE01, Q10N21, Q338N8, Q10M74, Q2QPW1, Q75KR1, Q8H4V1, P14654, P14656, Q4W8D0
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contains a high proportion of unphosphorylated CPD photolyase
L-GalLDH is attached to complex I of the mitochondrial electron transport chain
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contains a relatively high proportion of the phosphorylated CPD photolyase
additional information
OsPSS-1 localizes to organelles associated with exocytosis
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additional information
phosphorylation of CPD photolyase is involved in the translocation of this enzyme to organelles
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additional information
the white panicle1 mutant WP1 form of a Val-tRNA synthetase (OsValRS2) from Oryza sativa is targeted to both chloroplasts and mitochondria
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LINKS TO OTHER DATABASES (specific for Oryza sativa Japonica Group)
SILVA: 16S/18S rRNA, 23S/28S rRNA
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