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

KN538700.1_FGP039

Organism

Oryza longistaminata

Taxonomic ID

4528

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: 1213aa MW: 136625 Da PI: 6.8486

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KN538700.1_FGP039	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	56.9	3.5e-18	1093	1148	2	57
T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS Homeobox 2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 rk+ ++++eql++Le+++e +++++++ ++ LA+kl+++ rqV vWFqNrRa+ k+ KN538700.1_FGP039 1093 RKKLRLSEEQLTVLENMYEADSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKH 1148 778899***********************************************995 PP
2	HD-ZIP_I/II	97.7	1.2e-31	1093	1180	1	88
HD-ZIP_I/II 1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLr 88 +kk+rls+eq+++LE+++e++++L++ K+ la++L+++prqv+vWFqnrRARtk kq+E++++ Lkr+++ l++en+rL+ e+ ++ KN538700.1_FGP039 1093 RKKLRLSEEQLTVLENMYEADSNLDQALKQGLAEKLNIKPRQVEVWFQNRRARTKHKQIEEECKNLKRWLEDLNKENQRLKMEMMRVS 1180 69*******************************************************************************9998765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00862	6.1E-12	125	399	IPR000368	Sucrose synthase
TIGRFAMs	TIGR02468	0	138	1017	IPR012819	Sucrose phosphate synthase, plant
CDD	cd03800	9.96E-161	139	629	No hit	No description
SuperFamily	SSF53756	5.5E-69	150	629	No hit	No description
Gene3D	G3DSA:3.40.50.2000	2.5E-21	438	613	No hit	No description
Pfam	PF00534	9.4E-27	438	611	IPR001296	Glycosyl transferase, family 1
Pfam	PF05116	2.3E-16	773	973	IPR006380	Sucrose-phosphatase, N-terminal
Gene3D	G3DSA:1.10.10.60	5.1E-16	1081	1149	IPR009057	Homeodomain-like
SuperFamily	SSF46689	3.13E-16	1083	1150	IPR009057	Homeodomain-like
PROSITE profile	PS50071	16.277	1089	1149	IPR001356	Homeobox domain
SMART	SM00389	1.8E-15	1091	1153	IPR001356	Homeobox domain
CDD	cd00086	6.94E-15	1093	1150	No hit	No description
Pfam	PF00046	1.1E-15	1093	1148	IPR001356	Homeobox domain
PROSITE pattern	PS00027	0	1124	1147	IPR017970	Homeobox, conserved site
SMART	SM00340	0.0023	1149	1187	IPR003106	Leucine zipper, homeobox-associated

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:0005794	Cellular Component	Golgi apparatus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
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: 1213 aa Download sequence Send to blast
MNFNPTHYFV EEVVKGVDES DLHRTWIKLE LEGILRISAR RKEQEQVRRE TSEDLAEDLF 60 EGEKADTVGE LVQQDTPMKK KFQRNFSELT VSWSDENKEK KLYIVLIRSY TAYFTHWCHS 120 VYATKLQNFT EFLCSLFYFS LHGLVRGDNM ELGRDSDTGG QVKYVVELAR ALAMMPGVYR 180 VDLFTRQVSS PEVDWSYGEP TEMLTSGSTD GEGSGESAGA YIVRIPCGPR DKYLRKEALW 240 PYLQEFVDGA LAHILNMSKA LGEQVSNGKV VLPYVIHGHY ADAGDVAALL SGALNVPMVL 300 TGHSLGRNKL EQIMNQGRMS KEEIDSTYKI MRRIEGEELA LDAAELVITS TRQEIDEQWG 360 LYDGFDVKLE KVLRARARRG VSCHGRFMPR MVVIPPGMDF SSVVVPEDIS DGDDGKEFEI 420 ASPRSLPPIW AEVMRFLTNP HKPMILALSR PDPKKNITTL VKAFGECRPL RELANLILIM 480 GNRDDIDEMS AGNASVLTTV LKLIDKYDLY GSVAFPKHHK QSDVPEIYRL TGKMKGVFIN 540 PALVEPFGLT LIEAAAHGLP TVATKNGGPV DIKNALNNGL LVDPHDQHAI SDALLKLVAD 600 KNLWQECRKN GLRNIQLYSW PEHCRTYLTR IAGCRIRNPR WLMDTPADAA AEEEEALEDS 660 LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ DSVQRIMNKI KRSSPADTDG AKIPAEATAT 720 ATAGAMNKYP LLRRRRRLFV IAVDCYGDDG SASKRMLQVI QEVFRAVRSD SQMSRISGFA 780 LSTAMPLPET LKLLQLGKIP PTDFDALICG SGSEVYYPGT AQCVDAGGRL RPDQDYLLHI 840 NHRWSHDGAK QTIAKLAHDG SGTNVEPDVE SCNPHCVSFF IKDPNKVRTI DEMRERMRMR 900 GLRCHLMYCR NATRLQVVPL LASRSQALRY LFVRWGLSVG NMYLIVGEHG DTDHEEMLSG 960 LHKTVIIRGV TEKGSEQLVR SSGSYQREDV VPSESPLIAF TKGDLKADEI MRALKEVTKA 1020 ASGMDWQRPL CKTAYWFQSR VYTNMEEEEM TMLSLGVGAA SKHSISNRKF RLKEVTDHKF 1080 NPGDQDHNSG HARKKLRLSE EQLTVLENMY EADSNLDQAL KQGLAEKLNI KPRQVEVWFQ 1140 NRRARTKHKQ IEEECKNLKR WLEDLNKENQ RLKMEMMRVS RPVSTPHGST HNVSEVTVTC 1200 LSCNKSSYET STV

Sequence ? help Back to Top

Protein Sequence Length: 1213 aa Download sequence Send to blast

MNFNPTHYFV EEVVKGVDES DLHRTWIKLE LEGILRISAR RKEQEQVRRE TSEDLAEDLF  60
EGEKADTVGE LVQQDTPMKK KFQRNFSELT VSWSDENKEK KLYIVLIRSY TAYFTHWCHS  120
VYATKLQNFT EFLCSLFYFS LHGLVRGDNM ELGRDSDTGG QVKYVVELAR ALAMMPGVYR  180
VDLFTRQVSS PEVDWSYGEP TEMLTSGSTD GEGSGESAGA YIVRIPCGPR DKYLRKEALW  240
PYLQEFVDGA LAHILNMSKA LGEQVSNGKV VLPYVIHGHY ADAGDVAALL SGALNVPMVL  300
TGHSLGRNKL EQIMNQGRMS KEEIDSTYKI MRRIEGEELA LDAAELVITS TRQEIDEQWG  360
LYDGFDVKLE KVLRARARRG VSCHGRFMPR MVVIPPGMDF SSVVVPEDIS DGDDGKEFEI  420
ASPRSLPPIW AEVMRFLTNP HKPMILALSR PDPKKNITTL VKAFGECRPL RELANLILIM  480
GNRDDIDEMS AGNASVLTTV LKLIDKYDLY GSVAFPKHHK QSDVPEIYRL TGKMKGVFIN  540
PALVEPFGLT LIEAAAHGLP TVATKNGGPV DIKNALNNGL LVDPHDQHAI SDALLKLVAD  600
KNLWQECRKN GLRNIQLYSW PEHCRTYLTR IAGCRIRNPR WLMDTPADAA AEEEEALEDS  660
LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ DSVQRIMNKI KRSSPADTDG AKIPAEATAT  720
ATAGAMNKYP LLRRRRRLFV IAVDCYGDDG SASKRMLQVI QEVFRAVRSD SQMSRISGFA  780
LSTAMPLPET LKLLQLGKIP PTDFDALICG SGSEVYYPGT AQCVDAGGRL RPDQDYLLHI  840
NHRWSHDGAK QTIAKLAHDG SGTNVEPDVE SCNPHCVSFF IKDPNKVRTI DEMRERMRMR  900
GLRCHLMYCR NATRLQVVPL LASRSQALRY LFVRWGLSVG NMYLIVGEHG DTDHEEMLSG  960
LHKTVIIRGV TEKGSEQLVR SSGSYQREDV VPSESPLIAF TKGDLKADEI MRALKEVTKA  1020
ASGMDWQRPL CKTAYWFQSR VYTNMEEEEM TMLSLGVGAA SKHSISNRKF RLKEVTDHKF  1080
NPGDQDHNSG HARKKLRLSE EQLTVLENMY EADSNLDQAL KQGLAEKLNI KPRQVEVWFQ  1140
NRRARTKHKQ IEEECKNLKR WLEDLNKENQ RLKMEMMRVS RPVSTPHGST HNVSEVTVTC  1200
LSCNKSSYET STV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2r60_A	2e-53	157	631	31	456	Glycosyl transferase, group 1
2r66_A	2e-53	157	631	31	456	Glycosyl transferase, group 1
2r68_A	2e-53	157	631	31	456	Glycosyl transferase, group 1
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	731	737	LRRRRRL
2	1141	1149	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	KN538700.1_FGP039

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	A0A0E0N6U8	0.0	A0A0E0N6U8_ORYRU; Uncharacterized protein
STRING	ORUFI01G45310.1	0.0	(Oryza rufipogon)

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	1e-24	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]