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

OBART01G41950.1

Organism

Oryza barthii

Taxonomic ID

65489

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: 1223aa MW: 137956 Da PI: 8.0075

Description

HD-ZIP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OBART01G41950.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	49.6	6.9e-16	1124	1179	2	57
T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS Homeobox 2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 rk+ ++++eql++Le+++e ++++++ ++ LA+kl+++ rq vWFqNrRa+ k+ OBART01G41950.1 1124 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQFEVWFQNRRARTKH 1179 677889***********************************************995 PP
2	HD-ZIP_I/II	90.2	2.5e-29	1124	1208	1	85
HD-ZIP_I/II 1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeve 85 +kk+rls+eq+++LE+++e+ ++L++ K+ la++L+++prq +vWFqnrRARtk kq+E++++ Lkr+++ l++en+rL+ e OBART01G41950.1 1124 RKKLRLSEEQLTVLENMYEAGSNLDQALKQGLAEKLNIKPRQFEVWFQNRRARTKHKQIEEECKNLKRWLEGLNKENQRLKMELM 1208 69*******************************************************************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR02468	0	14	1047	IPR012819	Sucrose phosphate synthase, plant
CDD	cd03800	2.60E-162	170	659	No hit	No description
Pfam	PF00862	9.9E-13	171	434	IPR000368	Sucrose synthase
SuperFamily	SSF53756	1.53E-67	185	659	No hit	No description
Gene3D	G3DSA:3.40.50.2000	5.7E-19	473	643	No hit	No description
Pfam	PF00534	2.0E-23	473	641	IPR001296	Glycosyl transferase, family 1
Pfam	PF05116	2.4E-16	803	1003	IPR006380	Sucrose-phosphatase, N-terminal
SuperFamily	SSF46689	1.88E-14	1114	1181	IPR009057	Homeodomain-like
PROSITE profile	PS50071	15.24	1120	1180	IPR001356	Homeobox domain
SMART	SM00389	2.9E-11	1122	1184	IPR001356	Homeobox domain
Gene3D	G3DSA:1.10.10.60	6.6E-14	1124	1178	IPR009057	Homeodomain-like
Pfam	PF00046	2.2E-13	1124	1179	IPR001356	Homeobox domain
CDD	cd00086	3.20E-12	1124	1181	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005985	Biological Process	sucrose metabolic process
GO:0005634	Cellular Component	nucleus
GO:0005794	Cellular Component	Golgi apparatus
GO:0016021	Cellular Component	integral component of membrane
GO:0003677	Molecular Function	DNA binding
GO:0016157	Molecular Function	sucrose synthase activity
GO:0046524	Molecular Function	sucrose-phosphate synthase activity

Sequence ? help Back to Top
Protein Sequence Length: 1223 aa Download sequence Send to blast
MATWRRYWSP AAGAASPRGP HMNFNPTHYF VEEVVKGVDE SDLHRTWIKV VATRNARERS 60 TRLENMCWRI WHLARKKKQA CIDLSLSFSF FLVFMLELEG ILRISARRKE QEQVRRETSE 120 DLAEDLFEGE KADTVGELAQ QDTPMKKKFQ RNFSELTVSW SDENKEKKLY IVLISLHGLV 180 RGDNMELGRD SDTGGQVKYV VELARALAMM PGVYRVDLFT RQVSSPEVDW SYGEPTEMLT 240 SGSTDGEGSG ESAGAYIVRI PCGPRDKYLR KEALWPYLQE FVDGALAHIL NMSKALGEQV 300 SNGKLVLPYV IHGHYADAGD VAALLSGALN VPMVLTGHSL GRNKLEQIMK QGRMSKEEID 360 STYKIMRRIE GEELALDAAE LVITSTRQEI DEQWGLYDGF DVKLEKVLRA RARRGVSCHG 420 RFMPRMVVIP PGMDFSSVVV PEDTSDGDDG KDFEIASPRS LPPIWAEVMR FLTNPHKPMI 480 LALSRPDPKK NITTLVKAFG ECRPLRELAN LILIMGNRDD IDEMSAGNAS VLTTVLKLID 540 KYDLYGSVAF PKHHKQSDVP EIYRLTGKMK GVFINPALVE PFGLTLIEAA AHGLPIVATK 600 NGGPALNNGL LVDPHDQHAI ADALLKLVAD KNLWQECRKN GLRNIQLYSW PEHCRTYLTR 660 IAGCRIRNPR WLMDTPADAA AEEEEALEDS LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ 720 DSVQRIMNKI KRSSPADTDG AKIPAEAAAT ATSGAMNKYP LLRRRRRLFV IAVDCYGDDG 780 SASKRMLQVI QEVFRAVRSD SQMSRISGFA LSTAMPLPET LKLLQLGKIP PTDFDALICG 840 SGSEVYYPGT AQCVDAGGRL RPDQDYLLHI NHRWSHDGAK QTIAKLAHDG SGTNVEPDVE 900 SCNPHCVSFF IKDPNKVRTI DEMRERMRMR GLRCHLMYCR NATRLQVVPL LASRSQALRY 960 LFVRWGLSVG NMYLIVGEHG DTDHEEMLSG LHKTVIIRGV TEKGSEQLVR SSGSYQREDV 1020 VPSESPLIAF TKGDLKADEI MRALKEVTKA ASGMDWQRPL CKTAYWFQSR VYTNMEEKEE 1080 MTMLSLGVGA ASKHSISNRK FRLKEVTDHK FNLGDQDHNS GHVRKKLRLS EEQLTVLENM 1140 YEAGSNLDQA LKQGLAEKLN IKPRQFEVWF QNRRARTKHK QIEEECKNLK RWLEGLNKEN 1200 QRLKMELMRN AQKDCIKKGI QQW

Sequence ? help Back to Top

Protein Sequence Length: 1223 aa Download sequence Send to blast

MATWRRYWSP AAGAASPRGP HMNFNPTHYF VEEVVKGVDE SDLHRTWIKV VATRNARERS  60
TRLENMCWRI WHLARKKKQA CIDLSLSFSF FLVFMLELEG ILRISARRKE QEQVRRETSE  120
DLAEDLFEGE KADTVGELAQ QDTPMKKKFQ RNFSELTVSW SDENKEKKLY IVLISLHGLV  180
RGDNMELGRD SDTGGQVKYV VELARALAMM PGVYRVDLFT RQVSSPEVDW SYGEPTEMLT  240
SGSTDGEGSG ESAGAYIVRI PCGPRDKYLR KEALWPYLQE FVDGALAHIL NMSKALGEQV  300
SNGKLVLPYV IHGHYADAGD VAALLSGALN VPMVLTGHSL GRNKLEQIMK QGRMSKEEID  360
STYKIMRRIE GEELALDAAE LVITSTRQEI DEQWGLYDGF DVKLEKVLRA RARRGVSCHG  420
RFMPRMVVIP PGMDFSSVVV PEDTSDGDDG KDFEIASPRS LPPIWAEVMR FLTNPHKPMI  480
LALSRPDPKK NITTLVKAFG ECRPLRELAN LILIMGNRDD IDEMSAGNAS VLTTVLKLID  540
KYDLYGSVAF PKHHKQSDVP EIYRLTGKMK GVFINPALVE PFGLTLIEAA AHGLPIVATK  600
NGGPALNNGL LVDPHDQHAI ADALLKLVAD KNLWQECRKN GLRNIQLYSW PEHCRTYLTR  660
IAGCRIRNPR WLMDTPADAA AEEEEALEDS LMDVQDLSLR LSIDGERGSS MNDAPSSDPQ  720
DSVQRIMNKI KRSSPADTDG AKIPAEAAAT ATSGAMNKYP LLRRRRRLFV IAVDCYGDDG  780
SASKRMLQVI QEVFRAVRSD SQMSRISGFA LSTAMPLPET LKLLQLGKIP PTDFDALICG  840
SGSEVYYPGT AQCVDAGGRL RPDQDYLLHI NHRWSHDGAK QTIAKLAHDG SGTNVEPDVE  900
SCNPHCVSFF IKDPNKVRTI DEMRERMRMR GLRCHLMYCR NATRLQVVPL LASRSQALRY  960
LFVRWGLSVG NMYLIVGEHG DTDHEEMLSG LHKTVIIRGV TEKGSEQLVR SSGSYQREDV  1020
VPSESPLIAF TKGDLKADEI MRALKEVTKA ASGMDWQRPL CKTAYWFQSR VYTNMEEKEE  1080
MTMLSLGVGA ASKHSISNRK FRLKEVTDHK FNLGDQDHNS GHVRKKLRLS EEQLTVLENM  1140
YEAGSNLDQA LKQGLAEKLN IKPRQFEVWF QNRRARTKHK QIEEECKNLK RWLEGLNKEN  1200
QRLKMELMRN AQKDCIKKGI QQW

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2r60_A	2e-50	192	661	31	456	Glycosyl transferase, group 1
2r66_A	2e-50	192	661	31	456	Glycosyl transferase, group 1
2r68_A	2e-50	192	661	31	456	Glycosyl transferase, group 1
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	761	767	LRRRRRL
2	1172	1180	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	A0A0D3EXX4	0.0	A0A0D3EXX4_9ORYZ; Uncharacterized protein
STRING	OBART01G41950.1	0.0	(Oryza barthii)

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-23	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]