PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

OGLUM01G46130.1

Organism

Oryza glumaepatula

Taxonomic ID

40148

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

Family

HD-ZIP

Protein Properties

Length: 1267aa MW: 140786 Da PI: 7.7124

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OGLUM01G46130.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	55.6	9.3e-18	1168	1223	2	57
T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS Homeobox 2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 rk+ ++++eql++Le+++e ++++++ ++ LA+kl+++ rqV vWFqNrRa+ k+ OGLUM01G46130.1 1168 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKH 1223 677889***********************************************995 PP
2	HD-ZIP_I/II	93.6	2.1e-30	1168	1252	1	85
HD-ZIP_I/II 1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeve 85 +kk+rls+eq+++LE+++e+ ++L++ K+ la++L+++prqv+vWFqnrRARtk kq+E++++ Lkr+++ l++en+rL+ e OGLUM01G46130.1 1168 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKHKQIEEECKNLKRWLEGLNKENRRLKMELM 1252 69*******************************************************************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR02468	0	1	1091	IPR012819	Sucrose phosphate synthase, plant
CDD	cd03800	7.79E-162	211	700	No hit	No description
Pfam	PF00862	8.4E-13	212	475	IPR000368	Sucrose synthase
SuperFamily	SSF53756	2.83E-67	226	700	No hit	No description
Gene3D	G3DSA:3.40.50.2000	6.0E-19	514	684	No hit	No description
Pfam	PF00534	2.1E-23	514	682	IPR001296	Glycosyl transferase, family 1
Pfam	PF05116	2.5E-16	847	1047	IPR006380	Sucrose-phosphatase, N-terminal
SuperFamily	SSF46689	5.01E-16	1158	1225	IPR009057	Homeodomain-like
PROSITE profile	PS50071	15.888	1164	1224	IPR001356	Homeobox domain
SMART	SM00389	1.3E-14	1166	1228	IPR001356	Homeobox domain
Gene3D	G3DSA:1.10.10.60	1.0E-15	1168	1222	IPR009057	Homeodomain-like
Pfam	PF00046	3.1E-15	1168	1223	IPR001356	Homeobox domain
CDD	cd00086	3.71E-14	1168	1225	No hit	No description
PROSITE pattern	PS00027	0	1199	1222	IPR017970	Homeobox, conserved site

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005985	Biological Process	sucrose metabolic process
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0005794	Cellular Component	Golgi apparatus
GO:0016157	Molecular Function	sucrose synthase activity
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046524	Molecular Function	sucrose-phosphate synthase activity

Sequence ? help Back to Top
Protein Sequence Length: 1267 aa Download sequence Send to blast
MAGNEWINGY LEAILDSGGA AGGGGGGGGG GGGGGGGGGG GGGGGGDPRS PAAGAASPRG 60 PHMNFNPTHY FVEEVVKGVD ESDLHRTWIK VVATRNARER STRLENMCWR IWHLARKKKQ 120 ACIDLSLSFS FFLVFMLELE GILRISARRK EQEQVRRETS EDLAEDLFEG EKADTVGELA 180 QQDTPMKKKF QRNFSELTVS WSDENKEKKL YIVLISLHGL VRGDNMELGR DSDTGGQVKY 240 VVELARALAT MPGVYRVDLF TRQVSSPEVD WSYGEPTEML TSGSTDGEGS GESAGAYIVR 300 IPCGPRDKYL RKEALWPYLQ EFVDGALAHI LNMSKALGEQ VSNGKVVLPY 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 KNGGPALNNG LLVDPHDQHA 660 IADALLKLVA DKNLWQECRK NGLRNIQLYS WPEHCRTYLT RIAGCRIRNP RWLMDTPADA 720 AAEEEALEDS LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ DSVQRIMNKI KRSSPADTDG 780 AKIPAEAAAT ATATATSGAM NKYPLLRRRR RLFVIAVDCY GDDGSASKRM LQVIQEVFRA 840 VRSDSQMSRI SGFALSTAMP LPETLKLLQL GKIPPTDFDA LICGSGSEVY YPGTAQCVDA 900 GGRLRPDQDY LLHINHRWSH DGAKQTIAKL AHDGSGTNVE PDVESCNPHC VSFFIKDPNK 960 VRTIDEMRER MRMRGLRCHL MYCRNATRLQ VVPLLASRSQ ALRYLFVRWG LSVGNMYLIV 1020 GEHGDTDHEE MLSGLHKTVI IRGVTEKGSE QLVRSSGSYQ REDVVPSESP LIAFTKGDLK 1080 ADEIMRALKE VTKAASGMDW QRPLCKTAYW FQSRVYTNME EKEEMTMLSL GVGAASKHSI 1140 SNRKFRLKEV TDHKFNLGDQ DHNSGHVRKK LRLSEEQLTV LENMYEAGSN LDQALKQGLA 1200 EKLNIKPRQV EVWFQNRRAR TKHKQIEEEC KNLKRWLEGL NKENRRLKME LMRNAQKDCI 1260 KKGIQQS

Sequence ? help Back to Top

Protein Sequence Length: 1267 aa Download sequence Send to blast

MAGNEWINGY LEAILDSGGA AGGGGGGGGG GGGGGGGGGG GGGGGGDPRS PAAGAASPRG  60
PHMNFNPTHY FVEEVVKGVD ESDLHRTWIK VVATRNARER STRLENMCWR IWHLARKKKQ  120
ACIDLSLSFS FFLVFMLELE GILRISARRK EQEQVRRETS EDLAEDLFEG EKADTVGELA  180
QQDTPMKKKF QRNFSELTVS WSDENKEKKL YIVLISLHGL VRGDNMELGR DSDTGGQVKY  240
VVELARALAT MPGVYRVDLF TRQVSSPEVD WSYGEPTEML TSGSTDGEGS GESAGAYIVR  300
IPCGPRDKYL RKEALWPYLQ EFVDGALAHI LNMSKALGEQ VSNGKVVLPY 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 KNGGPALNNG LLVDPHDQHA  660
IADALLKLVA DKNLWQECRK NGLRNIQLYS WPEHCRTYLT RIAGCRIRNP RWLMDTPADA  720
AAEEEALEDS LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ DSVQRIMNKI KRSSPADTDG  780
AKIPAEAAAT ATATATSGAM NKYPLLRRRR RLFVIAVDCY GDDGSASKRM LQVIQEVFRA  840
VRSDSQMSRI SGFALSTAMP LPETLKLLQL GKIPPTDFDA LICGSGSEVY YPGTAQCVDA  900
GGRLRPDQDY LLHINHRWSH DGAKQTIAKL AHDGSGTNVE PDVESCNPHC VSFFIKDPNK  960
VRTIDEMRER MRMRGLRCHL MYCRNATRLQ VVPLLASRSQ ALRYLFVRWG LSVGNMYLIV  1020
GEHGDTDHEE MLSGLHKTVI IRGVTEKGSE QLVRSSGSYQ REDVVPSESP LIAFTKGDLK  1080
ADEIMRALKE VTKAASGMDW QRPLCKTAYW FQSRVYTNME EKEEMTMLSL GVGAASKHSI  1140
SNRKFRLKEV TDHKFNLGDQ DHNSGHVRKK LRLSEEQLTV LENMYEAGSN LDQALKQGLA  1200
EKLNIKPRQV EVWFQNRRAR TKHKQIEEEC KNLKRWLEGL NKENRRLKME LMRNAQKDCI  1260
KKGIQQS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2r60_A	3e-50	233	702	31	456	Glycosyl transferase, group 1
2r66_A	3e-50	233	702	31	456	Glycosyl transferase, group 1
2r68_A	3e-50	233	702	31	456	Glycosyl transferase, group 1
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	805	811	LRRRRRL
2	1216	1224	RRARTKHKQ

Functional Description ? help Back to Top
Source	Description
UniProt	Plays 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}.
UniProt	Plays 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
UniProt	INDUCTION: 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
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK121341	0.0	AK121341.1 Oryza sativa Japonica Group cDNA clone:J023120M11, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015621705.1	0.0	probable sucrose-phosphate synthase 1
Refseq	XP_015621706.1	0.0	probable sucrose-phosphate synthase 1
Swissprot	A2WYE9	0.0	SPSA1_ORYSI; Probable sucrose-phosphate synthase 1
Swissprot	Q0JGK4	0.0	SPSA1_ORYSJ; Probable sucrose-phosphate synthase 1
TrEMBL	A0A0D9YJ89	0.0	A0A0D9YJ89_9ORYZ; Uncharacterized protein
STRING	OGLUM01G46130.1	0.0	(Oryza glumipatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP906	6	6

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G06710.1	5e-25	homeobox from Arabidopsis thaliana

Publications ? help Back to Top
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] 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] 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] 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] 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] Jha AB,Dubey RS Carbohydrate metabolism in growing rice seedlings under arsenic toxicity. J. Plant Physiol., 2004. 161(7): p. 867-72 [PMID:15310076] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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]