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

NNU_003962-RA

Organism

Nelumbo nucifera

Taxonomic ID

4432

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo

Family

bHLH

Protein Properties

Length: 548aa MW: 59208.1 Da PI: 4.7909

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_003962-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.7	1.6e-11	364	406	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL A++Y+k+L NNU_003962-RA 364 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIDYLKEL 406 79*******************66......**************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.682	357	406	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.44E-16	360	426	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.8E-9	363	406	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-14	363	412	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.5E-15	364	419	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.91E-13	364	410	No hit	No description
CDD	cd04873	1.59E-6	477	518	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010440	Biological Process	stomatal lineage progression
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0050826	Biological Process	response to freezing
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 548 aa Download sequence Send to blast
MLSRVNGVVW MEEPGEEEDD VSWTRNNVGG GADNKDEMGS LSTFKSMLED DWYVNSNGNP 60 SHHDFQTIQS HQEIKDIAFS SNPSAETLLL QPVDSSSSCS PSSVFNIDPS QVQSFLPPKS 120 CFSSLLNVVC NNPFENGFDL GCDPGFLAPL QGTQSSGSPV LANRGSGVLS GFNGLTTDGQ 180 MSTPDLSSNS QFPSTRLLPL AENGCAVGGS FSSIGFGGFE GSANNLFLNR SKVLRPLEXF 240 PPVGAQPTLF QKRAAFRQNS AAAAGNSVLM GSESCRVSAS VEENKGKGEL EEDQEKKRKN 300 NEDDEVEEGS VDGSGLNYDS DEAMEINKVD EIVKNGGNSS IANSTVTGVD QKGKKKGLPA 360 KNLMAERRRR KKLNDRLYML RSVVPKISKM DRASILGDAI DYLKELLQRI NDLHNELEST 420 PPGSSMPSST SFHPLTPTPP TLPCRVKEEL CPSSLPSPNN QPARVEVRVR EGRAVNIHMF 480 CARRPGLLLS TMKALDTLGL DIQQAVISCF NGFALDVFRA EQCKEGPDVL PEDIKAVLLS 540 SAGFHGMM

Sequence ? help Back to Top

Protein Sequence Length: 548 aa Download sequence Send to blast

MLSRVNGVVW MEEPGEEEDD VSWTRNNVGG GADNKDEMGS LSTFKSMLED DWYVNSNGNP  60
SHHDFQTIQS HQEIKDIAFS SNPSAETLLL QPVDSSSSCS PSSVFNIDPS QVQSFLPPKS  120
CFSSLLNVVC NNPFENGFDL GCDPGFLAPL QGTQSSGSPV LANRGSGVLS GFNGLTTDGQ  180
MSTPDLSSNS QFPSTRLLPL AENGCAVGGS FSSIGFGGFE GSANNLFLNR SKVLRPLEXF  240
PPVGAQPTLF QKRAAFRQNS AAAAGNSVLM GSESCRVSAS VEENKGKGEL EEDQEKKRKN  300
NEDDEVEEGS VDGSGLNYDS DEAMEINKVD EIVKNGGNSS IANSTVTGVD QKGKKKGLPA  360
KNLMAERRRR KKLNDRLYML RSVVPKISKM DRASILGDAI DYLKELLQRI NDLHNELEST  420
PPGSSMPSST SFHPLTPTPP TLPCRVKEEL CPSSLPSPNN QPARVEVRVR EGRAVNIHMF  480
CARRPGLLLS TMKALDTLGL DIQQAVISCF NGFALDVFRA EQCKEGPDVL PEDIKAVLLS  540
SAGFHGMM

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	353	371	KKKGLPAKNLMAERRRRKK
2	365	372	ERRRRKKL

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. Binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA. Functions as a dimer with SPCH during stomatal initiation (PubMed:18641265, PubMed:28507175). {ECO:0000269\|PubMed:17416732, ECO:0000269\|PubMed:18641265, ECO:0000269\|PubMed:28507175}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By high-salt stress, cold stress and abscisic acid (ABA) treatment.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010250549.1	0.0	PREDICTED: transcription factor ICE1
Swissprot	Q9LSE2	1e-156	ICE1_ARATH; Transcription factor ICE1
TrEMBL	A0A1U7ZGF4	0.0	A0A1U7ZGF4_NELNU; transcription factor ICE1
STRING	XP_010250549.1	0.0	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G26744.4	1e-116	bHLH family protein

Publications ? help Back to Top
Chen Y, et al. Ambient temperature enhanced freezing tolerance of Chrysanthemum dichrum CdICE1 Arabidopsis via miR398. BMC Biol., 2013. 11: p. 121 [PMID:24350981] Xu F, et al. Increased drought tolerance through the suppression of ESKMO1 gene and overexpression of CBF-related genes in Arabidopsis. PLoS ONE, 2014. 9(9): p. e106509 [PMID:25184213] Jiang W,Wu J,Zhang Y,Yin L,Lu J Isolation of a WRKY30 gene from Muscadinia rotundifolia (Michx) and validation of its function under biotic and abiotic stresses. Protoplasma, 2015. 252(5): p. 1361-74 [PMID:25643917] Lang Z,Zhu J OST1 phosphorylates ICE1 to enhance plant cold tolerance. Sci China Life Sci, 2015. 58(3): p. 317-8 [PMID:25680856] Juan JX, et al. Agrobacterium-mediated transformation of tomato with the ICE1 transcription factor gene. Genet. Mol. Res., 2015. 14(1): p. 597-608 [PMID:25729995] Lee HG,Seo PJ The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in Arabidopsis. Plant J., 2015. 82(6): p. 962-77 [PMID:25912720] Horst RJ, et al. Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage. PLoS Genet., 2015. 11(7): p. e1005374 [PMID:26203655] Lee JH,Jung JH,Park CM INDUCER OF CBF EXPRESSION 1 integrates cold signals into FLOWERING LOCUS C-mediated flowering pathways in Arabidopsis. Plant J., 2015. 84(1): p. 29-40 [PMID:26248809] Wang CL,Zhang SC,Qi SD,Zheng CC,Wu CA Delayed germination of Arabidopsis seeds under chilling stress by overexpressing an abiotic stress inducible GhTPS11. Gene, 2016. 575(2 Pt 1): p. 206-12 [PMID:26325072] Lee JH,Park CM Integration of photoperiod and cold temperature signals into flowering genetic pathways in Arabidopsis. Plant Signal Behav, 2015. 10(11): p. e1089373 [PMID:26430754] Su F, et al. Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana. Front Plant Sci, 2015. 6: p. 810 [PMID:26483823] Klermund C, et al. LLM-Domain B-GATA Transcription Factors Promote Stomatal Development Downstream of Light Signaling Pathways in Arabidopsis thaliana Hypocotyls. Plant Cell, 2016. 28(3): p. 646-60 [PMID:26917680] Chen L, et al. NRPB3, the third largest subunit of RNA polymerase II, is essential for stomatal patterning and differentiation in Arabidopsis. Development, 2016. 143(9): p. 1600-11 [PMID:26989174] Lu X, et al. A novel Zea mays ssp. mexicana L. MYC-type ICE-like transcription factor gene ZmmICE1, enhances freezing tolerance in transgenic Arabidopsis thaliana. Plant Physiol. Biochem., 2017. 113: p. 78-88 [PMID:28189052] Deng C,Ye H,Fan M,Pu T,Yan J The rice transcription factors OsICE confer enhanced cold tolerance in transgenic Arabidopsis. Plant Signal Behav, 2017. 12(5): p. e1316442 [PMID:28414264] de Marcos A, et al. A Mutation in the bHLH Domain of the SPCH Transcription Factor Uncovers a BR-Dependent Mechanism for Stomatal Development. Plant Physiol., 2017. 174(2): p. 823-842 [PMID:28507175] Kim SH, et al. Phosphorylation of the transcriptional repressor MYB15 by mitogen-activated protein kinase 6 is required for freezing tolerance in Arabidopsis. Nucleic Acids Res., 2017. 45(11): p. 6613-6627 [PMID:28510716] Pal S, et al. TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation. Plant Physiol., 2017. 175(2): p. 916-926 [PMID:28827455] Zhao C, et al. MAP Kinase Cascades Regulate the Cold Response by Modulating ICE1 Protein Stability. Dev. Cell, 2017. 43(5): p. 618-629.e5 [PMID:29056551] Li H, et al. MPK3- and MPK6-Mediated ICE1 Phosphorylation Negatively Regulates ICE1 Stability and Freezing Tolerance in Arabidopsis. Dev. Cell, 2017. 43(5): p. 630-642.e4 [PMID:29056553] Lee JH,Jung JH,Park CM Light Inhibits COP1-Mediated Degradation of ICE Transcription Factors to Induce Stomatal Development in Arabidopsis. Plant Cell, 2017. 29(11): p. 2817-2830 [PMID:29070509] Liu Y,Zhou J MAPping Kinase Regulation of ICE1 in Freezing Tolerance. Trends Plant Sci., 2018. 23(2): p. 91-93 [PMID:29248419] Xie H, et al. Variation in ICE1 Methylation Primarily Determines Phenotypic Variation in Freezing Tolerance in Arabidopsis thaliana. Plant Cell Physiol., 2019. 60(1): p. 152-165 [PMID:30295898]