PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID BGIOSGA000239-PA
Common NameOsI_04951
Organism
Oryza sativa subsp. indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family HD-ZIP
Protein Properties Length: 1240aa    MW: 137701 Da    PI: 7.1485
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
BGIOSGA000239-PAgenomeRISView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox55.69e-1811701225257
                        T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
          Homeobox    2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57  
                        rk+ ++++eql++Le+++e  ++++++ ++ LA+kl+++ rqV vWFqNrRa+ k+
  BGIOSGA000239-PA 1170 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKH 1225
                        677889***********************************************995 PP
2HD-ZIP_I/II79.74.5e-2611701233164
       HD-ZIP_I/II    1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdye 64  
                        +kk+rls+eq+++LE+++e+ ++L++  K+ la++L+++prqv+vWFqnrRARtk kq+E++++
  BGIOSGA000239-PA 1170 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKHKQIEEECK 1233
                        69************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR02468011093IPR012819Sucrose phosphate synthase, plant
CDDcd038009.36E-164211705No hitNo description
PfamPF008621.0E-12212475IPR000368Sucrose synthase
SuperFamilySSF537561.88E-70226705No hitNo description
Gene3DG3DSA:3.40.50.20006.4E-22514689No hitNo description
PfamPF005341.9E-27514687IPR001296Glycosyl transferase, family 1
PfamPF051162.4E-168491049IPR006380Sucrose-phosphatase, N-terminal
SuperFamilySSF466894.71E-1611601227IPR009057Homeodomain-like
PROSITE profilePS5007115.88811661226IPR001356Homeobox domain
SMARTSM003891.3E-1411681230IPR001356Homeobox domain
CDDcd000862.21E-1411701227No hitNo description
Gene3DG3DSA:1.10.10.609.9E-1611701224IPR009057Homeodomain-like
PfamPF000463.0E-1511701225IPR001356Homeobox domain
PROSITE patternPS00027012011224IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005985Biological Processsucrose metabolic process
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005794Cellular ComponentGolgi apparatus
GO:0016157Molecular Functionsucrose synthase activity
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046524Molecular Functionsucrose-phosphate synthase activity
Sequence ? help Back to Top
Protein Sequence    Length: 1240 aa     Download sequence    Send to blast
MAGNEWINGY LEAILDSGGA AGGGGGGGGG GGGGGGGGGG GGGGGVDPRS PAAGAASPRG  60
PHMNFNPTHY FVEEVVKGVD ESDLHRTWIK VVATRNARER STRLENMCWR IWHLARKKKQ  120
ACIDLSLSFS FFLVFMLELE GILRISARRK EQEQVRRETS EDLAEDLFEG EKADTVGELA  180
QQDTPMKKKF QRNFSELTVS WSDENKEKKL YIVLISLHGL VRGDNMELGR DSDTGGQVKY  240
VVELARALAM MPGVYRVDLF TRQVSSPEVD WSYGEPTEML TSGSTDGEGS GESAGAYIVR  300
IPCGPRDKYL RKEALWPYLQ EFVDGALAHI LNMSKALGEQ VSNGKLVLPY VIHGHYADAG  360
DVAALLSGAL NVPMVLTGHS LGRNKLEQIM KQGRMSKEEI DSTYKIMRRI EGEELALDAA  420
ELVITSTRQE IDEQWGLYDG FDVKLEKVLR ARARRGVSCH GRFMPRMVVI PPGMDFSSVV  480
VPEDTSDGDD GKDFEIASPR SLPPIWAEVM RFLTNPHKPM ILALSRPDPK KNITTLVKAF  540
GECRPLRELA NLILIMGNRD DIDEMSAGNA SVLTTVLKLI DKYDLYGSVA FPKHHKQSDV  600
PEIYRLTGKM KGVFINPALV EPFGLTLIEA AAHGLPIVAT KNGGPVDIKN ALNNGLLVDP  660
HDQHAIADAL LKLVADKNLW QECRKNGLRN IQLYSWPEHC RTYLTRIAGC RIRNPRWLMD  720
TPADAAAEEE EALEDSLMDV QDLSLRLSID GERGSSMNDA PSSDPQDSVQ RIMNKIKRSS  780
PADTDGAKIP AEAAATATSG AMNKYPLLRR RRRLFVIAVD CYGDDGSASK RMLQVIQEVF  840
RAVRSDSQMS RISGFALSTA MPLPETLKLL QLGKIPPTDF DALICGSGSE VYYPGTAQCV  900
DAGGRLRPDQ DYLLHINHRW SHDGAKQTIA KLAHDGSGTN VEPDVESCNP HCVSFFIKDP  960
NKVRTIDEMR ERMRMRGLRC HLMYCRNATR LQVVPLLASR SQALRYLFVR WGLSVGNMYL  1020
IVGEHGDTDH EEMLSGLHKT VIIRGVTEKG SEQLVRSSGS YQREDVVPSE SPLIAFTKGD  1080
LKADEIMRAL KEVTKAASGM DWQWPLCKTA YWFQSRVYTN MEEKEEMTML SLGVGAASKH  1140
SISNRKFRLK EVTDHKFNLG DQDHNSGHVR KKLRLSEEQL TVLENMYEAG SNLDQALKQG  1200
LAEKLNIKPR QVEVWFQNRR ARTKHKQIEE ECKNRGGWRA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2r60_A3e-5223370731456Glycosyl transferase, group 1
2r66_A3e-5223370731456Glycosyl transferase, group 1
2r68_A3e-5223370731456Glycosyl transferase, group 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1807813LRRRRRL
212181226RRARTKHKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.34540.0flower| leaf| panicle| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO379909640.0
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Highly expressed in source leaves and at low levels in sink leaves. {ECO:0000269|PubMed:21683881}.
UniprotTISSUE SPECIFICITY: Expressed in germinating seeds. {ECO:0000269|PubMed:21683881}.
UniprotTISSUE SPECIFICITY: Expressed in leaves mesophyll cells, scutellum of germinating seedlings and pollen of immature inflorescences. {ECO:0000269|PubMed:11027714, ECO:0000269|PubMed:8666248}.
Functional Description ? help Back to Top
Source Description
UniProtPlays a role in photosynthetic sucrose synthesis by catalyzing the rate-limiting step of sucrose biosynthesis from UDP-glucose and fructose- 6-phosphate. Involved in the regulation of carbon partitioning in the leaves of plants. May regulate the synthesis of sucrose and therefore play a major role as a limiting factor in the export of photoassimilates out of the leaf. Plays a role for sucrose availability that is essential for plant growth and fiber elongation (By similarity). {ECO:0000250}.
UniProtPlays a role in photosynthetic sucrose synthesis by catalyzing the rate-limiting step of sucrose biosynthesis from UDP-glucose and fructose- 6-phosphate. Involved in the regulation of carbon partitioning in the leaves of plants. May regulate the synthesis of sucrose and therefore play a major role as a limiting factor in the export of photoassimilates out of the leaf. Plays a role for sucrose availability that is essential for plant growth and fiber elongation (By similarity). {ECO:0000250}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian-regulated, with the highest expression 1 hour before the beginning of light period (in 14 hours light/10 hours dark cycle). {ECO:0000269|PubMed:21683881}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1213410.0AK121341.1 Oryza sativa Japonica Group cDNA clone:J023120M11, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015621705.10.0probable sucrose-phosphate synthase 1
RefseqXP_015621706.10.0probable sucrose-phosphate synthase 1
SwissprotA2WYE90.0SPSA1_ORYSI; Probable sucrose-phosphate synthase 1
SwissprotQ0JGK40.0SPSA1_ORYSJ; Probable sucrose-phosphate synthase 1
TrEMBLB8A8E20.0B8A8E2_ORYSI; Uncharacterized protein
STRINGOGLUM01G46130.10.0(Oryza glumipatula)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP90666
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G06710.13e-18homeobox from Arabidopsis thaliana
Publications ? help Back to Top
  1. Chávez-Bárcenas AT, et al.
    Tissue-specific and developmental pattern of expression of the rice sps1 gene.
    Plant Physiol., 2000. 124(2): p. 641-54
    [PMID:11027714]
  2. Nakano H,Makino A,Mae T
    The Effect of Elevated Partial Pressures of CO2 on the Relationship between Photosynthetic Capacity and N Content in Rice Leaves.
    Plant Physiol., 1997. 115(1): p. 191-198
    [PMID:12223799]
  3. Makino A,Nakano H,Mae T
    Responses of Ribulose-1,5-Bisphosphate Carboxylase, Cytochrome f, and Sucrose Synthesis Enzymes in Rice Leaves to Leaf Nitrogen and Their Relationships to Photosynthesis.
    Plant Physiol., 1994. 105(1): p. 173-179
    [PMID:12232197]
  4. Ishimaru K,Ono K,Kashiwagi T
    Identification of a new gene controlling plant height in rice using the candidate-gene strategy.
    Planta, 2004. 218(3): p. 388-95
    [PMID:14534788]
  5. Ding J, et al.
    Validation of a rice specific gene, sucrose phosphate synthase, used as the endogenous reference gene for qualitative and real-time quantitative PCR detection of transgenes.
    J. Agric. Food Chem., 2004. 52(11): p. 3372-7
    [PMID:15161200]
  6. Jha AB,Dubey RS
    Carbohydrate metabolism in growing rice seedlings under arsenic toxicity.
    J. Plant Physiol., 2004. 161(7): p. 867-72
    [PMID:15310076]
  7. Yang L, et al.
    Estimating the copy number of transgenes in transformed rice by real-time quantitative PCR.
    Plant Cell Rep., 2005. 23(10-11): p. 759-63
    [PMID:15459795]
  8. Lutfiyya LL, et al.
    Phylogenetic and expression analysis of sucrose phosphate synthase isozymes in plants.
    J. Plant Physiol., 2007. 164(7): p. 923-33
    [PMID:16876912]
  9. Ishimaru K,Hirotsu N,Madoka Y,Kashiwagi T
    Quantitative trait loci for sucrose, starch, and hexose accumulation before heading in rice.
    Plant Physiol. Biochem., 2007 Oct-Nov. 45(10-11): p. 799-804
    [PMID:17845859]
  10. Li JY, et al.
    Effects of elevated CO2 on growth, carbon assimilation, photosynthate accumulation and related enzymes in rice leaves during sink-source transition.
    J Integr Plant Biol, 2008. 50(6): p. 723-32
    [PMID:18713413]
  11. Pattanagul W,Thitisaksakul M
    Effect of salinity stress on growth and carbohydrate metabolism in three rice (Oryza sativa L.) cultivars differing in salinity tolerance.
    Indian J. Exp. Biol., 2008. 46(10): p. 736-42
    [PMID:19024173]
  12. Jiang L, et al.
    International collaborative study of the endogenous reference gene, sucrose phosphate synthase (SPS), used for qualitative and quantitative analysis of genetically modified rice.
    J. Agric. Food Chem., 2009. 57(9): p. 3525-32
    [PMID:19326953]
  13. Ohara K,Sasaki K,Yazaki K
    Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.
    J. Exp. Bot., 2010. 61(10): p. 2683-92
    [PMID:20421194]
  14. Sharma S, et al.
    Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses.
    BMC Plant Biol., 2010. 10: p. 134
    [PMID:20591144]
  15. Wang C, et al.
    Evaluation of four genes in rice for their suitability as endogenous reference standards in quantitative PCR.
    J. Agric. Food Chem., 2010. 58(22): p. 11543-7
    [PMID:20961039]
  16. Okamura M, et al.
    Tissue specificity and diurnal change in gene expression of the sucrose phosphate synthase gene family in rice.
    Plant Sci., 2011. 181(2): p. 159-66
    [PMID:21683881]
  17. Zhu C, et al.
    The temporal and species dynamics of photosynthetic acclimation in flag leaves of rice (Oryza sativa) and wheat (Triticum aestivum) under elevated carbon dioxide.
    Physiol Plant, 2012. 145(3): p. 395-405
    [PMID:22268610]
  18. Mishra P,Dubey RS
    Excess nickel modulates activities of carbohydrate metabolizing enzymes and induces accumulation of sugars by upregulating acid invertase and sucrose synthase in rice seedlings.
    Biometals, 2013. 26(1): p. 97-111
    [PMID:23179408]
  19. Saad AS, et al.
    A rice stress-responsive NAC gene enhances tolerance of transgenic wheat to drought and salt stresses.
    Plant Sci., 2013. 203-204: p. 33-40
    [PMID:23415326]
  20. Yonekura M, et al.
    The promoter activities of sucrose phosphate synthase genes in rice, OsSPS1 and OsSPS11, are controlled by light and circadian clock, but not by sucrose.
    Front Plant Sci, 2013. 4: p. 31
    [PMID:23460029]
  21. Choudhury B,Mitra S,Biswas AK
    Regulation of sugar metabolism in rice (Oryza sativa L.) seedlings under arsenate toxicity and its improvement by phosphate.
    Physiol Mol Biol Plants, 2010. 16(1): p. 59-68
    [PMID:23572955]
  22. Hirose T, et al.
    Analysis of gene-disruption mutants of a sucrose phosphate synthase gene in rice, OsSPS1, shows the importance of sucrose synthesis in pollen germination.
    Plant Sci., 2014. 225: p. 102-6
    [PMID:25017165]
  23. Zhang F,Wang L,Wang R,Ying Y,Wu J
    Simple screening strategy with only water bath needed for the identification of insect-resistant genetically modified rice.
    Anal. Chem., 2015. 87(3): p. 1523-6
    [PMID:25582220]
  24. Wang X,Chen X,Xu J,Dai C,Shen W
    Degradation and detection of transgenic Bacillus thuringiensis DNA and proteins in flour of three genetically modified rice events submitted to a set of thermal processes.
    Food Chem. Toxicol., 2015. 84: p. 89-98
    [PMID:26277627]
  25. Li L, et al.
    A novel reference plasmid for the qualitative detection of genetically modified rice in food and feed.
    Biomed Res Int, 2015. 2015: p. 948297
    [PMID:26495318]
  26. Valdez-Alarcón JJ,Ferrando M,Salerno G,Jimenez-Moraila B,Herrera-Estrella L
    Characterization of a rice sucrose-phosphate synthase-encoding gene.
    Gene, 1996. 170(2): p. 217-22
    [PMID:8666248]