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

RrC1984_p3

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

bHLH

Protein Properties

Length: 510aa MW: 54197.6 Da PI: 5.0233

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1984_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.8	1.4e-11	326	368	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL A++Y+k+L RrC1984_p3 326 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIDYLKEL 368 79*******************66......**************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.866	319	368	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.18E-16	322	389	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.4E-9	325	368	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-14	325	374	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.25E-13	326	372	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.5E-15	326	381	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	8.19E-7	439	499	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: 510 aa Download sequence Send to blast
MVLDGNGGGV WLGGGGGGGG GERVQEEENE EASWGRNQED GGGGGSLSHQ FKPMLESGGG 60 DWFSSNQPHP QDLQMLQSQQ DFRFLGGFGF NPNDNLLLLQ HSMDSSSSCS PSQAFTLDPS 120 QSSFLAAAAN NKSCLLNVPS STNPFDNAFE FGSDSGFLGQ IQAPVSMGFG SLTQLGSSVP 180 DFLSARSLLP PENNNTTPLC GGGGGGGFTP LELEGFGSPA SFVGSRAKVL KPLEVLASSG 240 AQPTLFQKRA AMRQSSGSKM GNSESSGMMR RLSDDGEMDE TGIEVSGLNY ESDELNESGK 300 ASESVQNGGG GGGKGKKKGM PAKNLMAERR RRKKLNDRLY MLRSVVPKIS KMDRASILGD 360 AIDYLKELLQ RINDLHNELE STPNGSLPPT SSSFHPLTPT PQTLSCRVKE ELCPSSLPSP 420 KGQQARVEVR LREGRAVNIH MFCGRRPGLL LATMKALDNL GLDVQQAVIS CFNGFALDVF 480 RAEQCQEGQE ILPDQIKAVL FDTAGYAGMI

Sequence ? help Back to Top

Protein Sequence Length: 510 aa Download sequence Send to blast

MVLDGNGGGV WLGGGGGGGG GERVQEEENE EASWGRNQED GGGGGSLSHQ FKPMLESGGG  60
DWFSSNQPHP QDLQMLQSQQ DFRFLGGFGF NPNDNLLLLQ HSMDSSSSCS PSQAFTLDPS  120
QSSFLAAAAN NKSCLLNVPS STNPFDNAFE FGSDSGFLGQ IQAPVSMGFG SLTQLGSSVP  180
DFLSARSLLP PENNNTTPLC GGGGGGGFTP LELEGFGSPA SFVGSRAKVL KPLEVLASSG  240
AQPTLFQKRA AMRQSSGSKM GNSESSGMMR RLSDDGEMDE TGIEVSGLNY ESDELNESGK  300
ASESVQNGGG GGGKGKKKGM PAKNLMAERR RRKKLNDRLY MLRSVVPKIS KMDRASILGD  360
AIDYLKELLQ RINDLHNELE STPNGSLPPT SSSFHPLTPT PQTLSCRVKE ELCPSSLPSP  420
KGQQARVEVR LREGRAVNIH MFCGRRPGLL LATMKALDNL GLDVQQAVIS CFNGFALDVF  480
RAEQCQEGQE ILPDQIKAVL FDTAGYAGMI

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	315	333	KKKGMPAKNLMAERRRRKK
2	327	334	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.

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	HQ857208	0.0	HQ857208.2 Brassica juncea inducer of CBF expression 1 (ICE1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018484498.1	0.0	PREDICTED: LOW QUALITY PROTEIN: transcription factor ICE1
Swissprot	Q9LSE2	0.0	ICE1_ARATH; Transcription factor ICE1
TrEMBL	A0A397Z3C2	0.0	A0A397Z3C2_BRACM; Uncharacterized protein
STRING	Bo7g083870.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1952	27	82

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G26744.4	0.0	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]