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

Jcr4S02193.10

Organism

Jatropha curcas

Taxonomic ID

180498

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Crotonoideae; Jatropheae; Jatropha

Family

NF-YB

Protein Properties

Length: 651aa MW: 71214.4 Da PI: 7.3274

Description

NF-YB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Jcr4S02193.10	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YB	41.8	2.5e-13	13	101	5	88
NF-YB 5 drflPianvsrimkkvlPa.....nakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylk 88 ++lP a v ri+k l + + + kda e + fi ++++ a+d c++ +r+tin+dd+l al ++ f ++veplk+ lk Jcr4S02193.10 13 AEELPKAIVRRIVKDKLSQcspdgDLIVHKDALVAFSESARIFIHYLSATANDICKESRRQTINADDVLKALEEIEFPEFVEPLKASLK 101 5689********9986521211335789*****************************************************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.20.10	1.4E-28	7	155	IPR009072	Histone-fold
Pfam	PF00808	4.6E-11	15	84	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
SuperFamily	SSF47113	1.1E-22	16	145	IPR009072	Histone-fold
Gene3D	G3DSA:3.80.10.10	8.8E-54	204	475	IPR032675	Leucine-rich repeat domain, L domain-like
SuperFamily	SSF52058	5.83E-22	208	375	IPR032675	Leucine-rich repeat domain, L domain-like
SMART	SM00369	180	251	275	IPR003591	Leucine-rich repeat, typical subtype
PROSITE profile	PS51450	5.148	253	275	IPR001611	Leucine-rich repeat
PROSITE profile	PS51450	4.855	290	312	IPR001611	Leucine-rich repeat
SuperFamily	SSF52058	2.27E-49	328	645	IPR032675	Leucine-rich repeat domain, L domain-like
PROSITE profile	PS51450	4.516	387	409	IPR001611	Leucine-rich repeat
SMART	SM00369	0.52	433	457	IPR003591	Leucine-rich repeat, typical subtype
PROSITE profile	PS51450	5.486	435	457	IPR001611	Leucine-rich repeat
Gene3D	G3DSA:3.80.10.10	1.6E-31	481	612	IPR032675	Leucine-rich repeat domain, L domain-like
SMART	SM00369	300	496	520	IPR003591	Leucine-rich repeat, typical subtype
PROSITE profile	PS51450	4.609	570	591	IPR001611	Leucine-rich repeat
SMART	SM00369	240	592	615	IPR003591	Leucine-rich repeat, typical subtype
Pfam	PF00560	0.5	594	612	IPR001611	Leucine-rich repeat
PROSITE profile	PS51450	7.319	594	616	IPR001611	Leucine-rich repeat

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 651 aa Download sequence Send to blast
MESENVEKVV SEAEELPKAI VRRIVKDKLS QCSPDGDLIV HKDALVAFSE SARIFIHYLS 60 ATANDICKES RRQTINADDV LKALEEIEFP EFVEPLKASL KGNLYDVTXF KRKNAEKKAV 120 ASENGKKAGA SETQEVKKKR KVEEEPSQKR ASKQKKGEIG RLAQVRIEYE PGHMLMKSSI 180 PVKPAIAILK SSLKGPDGLG LENWKPLTES FSAHCSFSGV ACDKDSRVRL ENLVLAADNL 240 TGRLPVEMAN LTSLKILNIS NNLFTGHFPG EITVGMTKLE MPESYSDIQS LEYFALNGNG 300 LTGKIPASLA CLQNLKYMYL GHYNAYEGGI PSEFGSLSLL QVLDIASCNV TGEIPASLGH 360 LGHLHYLYLQ VYSLCGTIPH ELSSLTGLKI IDLSLNELTG DFPWSFFSRL NITFINLFLN 420 SLFGPIPSSI SDLPNLEVLH LCGNNFTSEL PKNLGQNQKI KDLDVSFNHL PGNIPRNLCK 480 GGNGITGRIS PAISKLQNLK ILLPDRNRLY GEIPAQVFHL KLPSGINISR NNLSGAIPAS 540 ISNCTSITLI DFSGNGLTGE IPSGISALKN LGTFDVSQNH LSGQLPIETQ YMSSLTKLDV 600 SNNNLSGKIP ASEQLLVFDD SSFSGNPKLC PARNISCQYL PLISIFKPWS Q

Sequence ? help Back to Top

Protein Sequence Length: 651 aa Download sequence Send to blast

MESENVEKVV SEAEELPKAI VRRIVKDKLS QCSPDGDLIV HKDALVAFSE SARIFIHYLS  60
ATANDICKES RRQTINADDV LKALEEIEFP EFVEPLKASL KGNLYDVTXF KRKNAEKKAV  120
ASENGKKAGA SETQEVKKKR KVEEEPSQKR ASKQKKGEIG RLAQVRIEYE PGHMLMKSSI  180
PVKPAIAILK SSLKGPDGLG LENWKPLTES FSAHCSFSGV ACDKDSRVRL ENLVLAADNL  240
TGRLPVEMAN LTSLKILNIS NNLFTGHFPG EITVGMTKLE MPESYSDIQS LEYFALNGNG  300
LTGKIPASLA CLQNLKYMYL GHYNAYEGGI PSEFGSLSLL QVLDIASCNV TGEIPASLGH  360
LGHLHYLYLQ VYSLCGTIPH ELSSLTGLKI IDLSLNELTG DFPWSFFSRL NITFINLFLN  420
SLFGPIPSSI SDLPNLEVLH LCGNNFTSEL PKNLGQNQKI KDLDVSFNHL PGNIPRNLCK  480
GGNGITGRIS PAISKLQNLK ILLPDRNRLY GEIPAQVFHL KLPSGINISR NNLSGAIPAS  540
ISNCTSITLI DFSGNGLTGE IPSGISALKN LGTFDVSQNH LSGQLPIETQ YMSSLTKLDV  600
SNNNLSGKIP ASEQLLVFDD SSFSGNPKLC PARNISCQYL PLISIFKPWS Q

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5gqr_B	1e-61	201	612	22	571	Leucine-rich repeat receptor-like protein kinase TDR
5gr9_B	1e-61	201	612	23	572	Leucine-rich repeat receptor-like protein kinase TDR
5jfi_A	2e-61	201	612	24	573	Leucine-rich repeat receptor-like protein kinase TDR
5jfi_B	2e-61	201	612	24	573	Leucine-rich repeat receptor-like protein kinase TDR
5jfk_A	2e-61	201	612	24	573	Leucine-rich repeat receptor-like protein kinase TDR
5jfk_B	2e-61	201	612	24	573	Leucine-rich repeat receptor-like protein kinase TDR
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	136	141	KKKRKV

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the detection of CLV3 and CLV3-like (CLE) peptides, that act as extracellular signals regulating meristem maintenance. Acts with CLV3p as a ligand-receptor pair in a signal transduction pathway coordinating growth between adjacent meristematic regions and controlling the balance between meristem cell proliferation and differentiation. {ECO:0000269\|PubMed:19933383}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021678075.1	1e-157	receptor protein kinase CLAVATA1-like
Swissprot	Q9SYQ8	1e-127	CLV1_ARATH; Receptor protein kinase CLAVATA1
TrEMBL	A0A2C9V1Z1	1e-145	A0A2C9V1Z1_MANES; Uncharacterized protein
STRING	cassava4.1_026756m	1e-146	(Manihot esculenta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF11863	32	36

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G27470.1	1e-40	nuclear factor Y, subunit B11

Publications ? help Back to Top
Trotochaud AE,Hao T,Wu G,Yang Z,Clark SE The CLAVATA1 receptor-like kinase requires CLAVATA3 for its assembly into a signaling complex that includes KAPP and a Rho-related protein. Plant Cell, 1999. 11(3): p. 393-406 [PMID:10072399] Williams RW,Clark SE,Meyerowitz EM Genetic and physical characterization of a region of Arabidopsis chromosome 1 containing the CLAVATA1 gene. Plant Mol. Biol., 1999. 39(1): p. 171-6 [PMID:10080719] Fletcher JC,Brand U,Running MP,Simon R,Meyerowitz EM Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science, 1999. 283(5409): p. 1911-4 [PMID:10082464] Li J,Smith GP,Walker JC Kinase interaction domain of kinase-associated protein phosphatase, a phosphoprotein-binding domain. Proc. Natl. Acad. Sci. U.S.A., 1999. 96(14): p. 7821-6 [PMID:10393905] Jeong S,Trotochaud AE,Clark SE The Arabidopsis CLAVATA2 gene encodes a receptor-like protein required for the stability of the CLAVATA1 receptor-like kinase. Plant Cell, 1999. 11(10): p. 1925-34 [PMID:10521522] Yamamoto E,Karakaya HC,Knap HT Molecular characterization of two soybean homologs of Arabidopsis thaliana CLAVATA1 from the wild type and fasciation mutant. Biochim. Biophys. Acta, 2000. 1491(1-3): p. 333-40 [PMID:10760600] Trotochaud AE,Jeong S,Clark SE CLAVATA3, a multimeric ligand for the CLAVATA1 receptor-kinase. Science, 2000. 289(5479): p. 613-7 [PMID:10915623] Yamamoto E,Knap HT Soybean receptor-like protein kinase genes: paralogous divergence of a gene family. Mol. Biol. Evol., 2001. 18(8): p. 1522-31 [PMID:11470843] Rivas S,Romeis T,Jones JD The Cf-9 disease resistance protein is present in an approximately 420-kilodalton heteromultimeric membrane-associated complex at one molecule per complex. Plant Cell, 2002. 14(3): p. 689-702 [PMID:11910014] Rojo E,Sharma VK,Kovaleva V,Raikhel NV,Fletcher JC CLV3 is localized to the extracellular space, where it activates the Arabidopsis CLAVATA stem cell signaling pathway. Plant Cell, 2002. 14(5): p. 969-77 [PMID:12034890] Diévart A, et al. CLAVATA1 dominant-negative alleles reveal functional overlap between multiple receptor kinases that regulate meristem and organ development. Plant Cell, 2003. 15(5): p. 1198-211 [PMID:12724544] Martynov VV,Tsvetkov IL,Khavkin EE [Orthologs of arabidopsis CLAVATA 1 gene in cultivated Brassicaceae plants]. Ontogenez, 2004 Jan-Feb. 35(1): p. 41-6 [PMID:15027212] Schnabel E,Journet EP,de Carvalho-Niebel F,Duc G,Frugoli J The Medicago truncatula SUNN gene encodes a CLV1-like leucine-rich repeat receptor kinase that regulates nodule number and root length. Plant Mol. Biol., 2005. 58(6): p. 809-822 [PMID:16240175] DeYoung BJ, et al. The CLAVATA1-related BAM1, BAM2 and BAM3 receptor kinase-like proteins are required for meristem function in Arabidopsis. Plant J., 2006. 45(1): p. 1-16 [PMID:16367950] Ni J,Clark SE Evidence for functional conservation, sufficiency, and proteolytic processing of the CLAVATA3 CLE domain. Plant Physiol., 2006. 140(2): p. 726-33 [PMID:16407446] Chu H, et al. The floral organ number4 gene encoding a putative ortholog of Arabidopsis CLAVATA3 regulates apical meristem size in rice. Plant Physiol., 2006. 142(3): p. 1039-52 [PMID:17012407] Suzaki T, et al. Conservation and diversification of meristem maintenance mechanism in Oryza sativa: Function of the FLORAL ORGAN NUMBER2 gene. Plant Cell Physiol., 2006. 47(12): p. 1591-602 [PMID:17056620] Ding Z, et al. Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase. Biochemistry, 2007. 46(10): p. 2684-96 [PMID:17302430] Ogawa M,Shinohara H,Sakagami Y,Matsubayashi Y Arabidopsis CLV3 peptide directly binds CLV1 ectodomain. Science, 2008. 319(5861): p. 294 [PMID:18202283] Furner I,Ellis L,Bakht S,Mirza B,Sheikh M CAUT lines: a novel resource for studies of cell autonomy in Arabidopsis. Plant J., 2008. 53(4): p. 645-60 [PMID:18269574] Müller R,Bleckmann A,Simon R The receptor kinase CORYNE of Arabidopsis transmits the stem cell-limiting signal CLAVATA3 independently of CLAVATA1. Plant Cell, 2008. 20(4): p. 934-46 [PMID:18381924] Deyoung BJ,Clark SE BAM receptors regulate stem cell specification and organ development through complex interactions with CLAVATA signaling. Genetics, 2008. 180(2): p. 895-904 [PMID:18780746] Kondo T,Nakamura T,Yokomine K,Sakagami Y Dual assay for MCLV3 activity reveals structure-activity relationship of CLE peptides. Biochem. Biophys. Res. Commun., 2008. 377(1): p. 312-6 [PMID:18848920] Miwa H, et al. The receptor-like kinase SOL2 mediates CLE signaling in Arabidopsis. Plant Cell Physiol., 2008. 49(11): p. 1752-7 [PMID:18854335] Ohyama K,Shinohara H,Ogawa-Ohnishi M,Matsubayashi Y A glycopeptide regulating stem cell fate in Arabidopsis thaliana. Nat. Chem. Biol., 2009. 5(8): p. 578-80 [PMID:19525968] Miwa H,Tamaki T,Fukuda H,Sawa S Evolution of CLE signaling: origins of the CLV1 and SOL2/CRN receptor diversity. Plant Signal Behav, 2009. 4(6): p. 477-81 [PMID:19816140] Zhu Y, et al. Analysis of interactions among the CLAVATA3 receptors reveals a direct interaction between CLAVATA2 and CORYNE in Arabidopsis. Plant J., 2010. 61(2): p. 223-33 [PMID:19843317] Bleckmann A,Weidtkamp-Peters S,Seidel CA,Simon R Stem cell signaling in Arabidopsis requires CRN to localize CLV2 to the plasma membrane. Plant Physiol., 2010. 152(1): p. 166-76 [PMID:19933383] Wang G,Fiers M CLE peptide signaling during plant development. Protoplasma, 2010. 240(1-4): p. 33-43 [PMID:20016993] Shinohara H,Matsubayashi Y Arabinosylated glycopeptide hormones: new insights into CLAVATA3 structure. Curr. Opin. Plant Biol., 2010. 13(5): p. 515-9 [PMID:20580598] Guo Y,Han L,Hymes M,Denver R,Clark SE CLAVATA2 forms a distinct CLE-binding receptor complex regulating Arabidopsis stem cell specification. Plant J., 2010. 63(6): p. 889-900 [PMID:20626648] Meng L,Feldman LJ CLE14/CLE20 peptides may interact with CLAVATA2/CORYNE receptor-like kinases to irreversibly inhibit cell division in the root meristem of Arabidopsis. Planta, 2010. 232(5): p. 1061-74 [PMID:20697738] Song X,Guo P,Li C,Liu CM The cysteine pairs in CLV2 are not necessary for sensing the CLV3 peptide in shoot and root meristems. J Integr Plant Biol, 2010. 52(9): p. 774-81 [PMID:20738721] Guo Y,Clark SE Membrane distributions of two ligand-binding receptor complexes in the CLAVATA pathway. Plant Signal Behav, 2010. 5(11): p. 1442-5 [PMID:21051944] Lee H,Chah OK,Sheen J Stem-cell-triggered immunity through CLV3p-FLS2 signalling. Nature, 2011. 473(7347): p. 376-9 [PMID:21499263] Okamoto S,Nakagawa T,Kawaguchi M Expression and functional analysis of a CLV3-like gene in the model legume Lotus japonicus. Plant Cell Physiol., 2011. 52(7): p. 1211-21 [PMID:21652543] Replogle A, et al. Synergistic interaction of CLAVATA1, CLAVATA2, and RECEPTOR-LIKE PROTEIN KINASE 2 in cyst nematode parasitism of Arabidopsis. Mol. Plant Microbe Interact., 2013. 26(1): p. 87-96 [PMID:22835273] Stahl Y, et al. Moderation of Arabidopsis root stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 receptor kinase complexes. Curr. Biol., 2013. 23(5): p. 362-71 [PMID:23394827] Liebrand TW, et al. Receptor-like kinase SOBIR1/EVR interacts with receptor-like proteins in plant immunity against fungal infection. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(24): p. 10010-5 [PMID:23716655] Wong CE,Singh MB,Bhalla PL Spatial expression of CLAVATA3 in the shoot apical meristem suggests it is not a stem cell marker in soybean. J. Exp. Bot., 2013. 64(18): p. 5641-9 [PMID:24179098] Araya T, et al. CLE-CLAVATA1 peptide-receptor signaling module regulates the expansion of plant root systems in a nitrogen-dependent manner. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(5): p. 2029-34 [PMID:24449877] Zhou F,Roy B,Dunlap JR,Enganti R,von Arnim AG Translational control of Arabidopsis meristem stability and organogenesis by the eukaryotic translation factor eIF3h. PLoS ONE, 2014. 9(4): p. e95396 [PMID:24736281] Guo X, et al. Enhanced resistance to soybean cyst nematode Heterodera glycines in transgenic soybean by silencing putative CLE receptors. Plant Biotechnol. J., 2015. 13(6): p. 801-10 [PMID:25581705] Shinohara H,Matsubayashi Y Reevaluation of the CLV3-receptor interaction in the shoot apical meristem: dissection of the CLV3 signaling pathway from a direct ligand-binding point of view. Plant J., 2015. 82(2): p. 328-36 [PMID:25754504] Nimchuk ZL,Zhou Y,Tarr PT,Peterson BA,Meyerowitz EM Plant stem cell maintenance by transcriptional cross-regulation of related receptor kinases. Development, 2015. 142(6): p. 1043-9 [PMID:25758219] Araya T,von Wirén N,Takahashi H CLE peptides regulate lateral root development in response to nitrogen nutritional status of plants. Plant Signal Behav, 2014. 9(7): p. e29302 [PMID:25763500] Poulios S,Vlachonasios KE Synergistic action of histone acetyltransferase GCN5 and receptor CLAVATA1 negatively affects ethylene responses in Arabidopsis thaliana. J. Exp. Bot., 2016. 67(3): p. 905-18 [PMID:26596766] Chou H,Zhu Y,Ma Y,Berkowitz GA The CLAVATA signaling pathway mediating stem cell fate in shoot meristems requires Ca(2+) as a secondary cytosolic messenger. Plant J., 2016. 85(4): p. 494-506 [PMID:26756833] Adibi M,Yoshida S,Weijers D,Fleck C Centering the Organizing Center in the Arabidopsis thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization. PLoS ONE, 2016. 11(2): p. e0147830 [PMID:26872130] Hanemian M, et al. Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. New Phytol., 2016. 211(2): p. 502-15 [PMID:26990325] Gursanscky NR, et al. MOL1 is required for cambium homeostasis in Arabidopsis. Plant J., 2016. 86(3): p. 210-20 [PMID:26991973] Nimchuk ZL CLAVATA1 controls distinct signaling outputs that buffer shoot stem cell proliferation through a two-step transcriptional compensation loop. PLoS Genet., 2017. 13(3): p. e1006681 [PMID:28355208] Clark SE,Williams RW,Meyerowitz EM The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell, 1997. 89(4): p. 575-85 [PMID:9160749] Williams RW,Wilson JM,Meyerowitz EM A possible role for kinase-associated protein phosphatase in the Arabidopsis CLAVATA1 signaling pathway. Proc. Natl. Acad. Sci. U.S.A., 1997. 94(19): p. 10467-72 [PMID:9294234] Stone JM,Trotochaud AE,Walker JC,Clark SE Control of meristem development by CLAVATA1 receptor kinase and kinase-associated protein phosphatase interactions Plant Physiol., 1998. 117(4): p. 1217-25 [PMID:9701578]