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

orange1.1g011398m

Common Name

CISIN_1g011370mg, LOC102620321

Organism

Citrus sinensis

Taxonomic ID

2711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

bHLH

Protein Properties

Length: 488aa MW: 53696.1 Da PI: 5.2326

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g011398m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.9	1.4e-11	307	349	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL A++Y+k+L orange1.1g011398m 307 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIDYLKEL 349 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	300	349	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.44E-16	303	368	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.2E-9	306	349	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-14	306	355	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.3E-15	307	362	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.21E-12	307	353	No hit	No description
CDD	cd04873	2.17E-7	416	457	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 488 aa Download sequence Send to blast
MVLEPNGAVW MEGEEEQPLS VSWTTAAAAT ATTTARATTE PKEDEMHVNA VSLSGFKSIL 60 DTDWFLNSTL NNPPQDFTNT TGLLETHQEL RAFNAFQETN LFFQPIESHP FTLNPTHSLL 120 PPNNNDNNSN SHLPFVSGFD LGGEAAGFIQ PASGFMGLTT TQICATNDSD FHGFGSSYSN 180 CFDNLEGLFF NSNSKAKVCS QSQPTLFEKR AALRQSSGKL ENLEILGGNL LLENIKCRKN 240 EEASVDISSL NYESDEYNNN NNNNNASNDN NVNGKVDESV KNWNAGGSAT VGDNKGKRKG 300 LPAKNLMAER RRRKKLNDRL YMLRSVVPKI SKMDRASILG DAIDYLKELL QRINDLHNEL 360 ESTPTGSLMQ PSTSIQPMTP TPPTLPCRVK EEISRSPTGE AARVEVRIRE GRAVNIHMFC 420 ARRPGLLLST MRALDSLGLD IQQAVISCFN GFALDVFRAE QCREGQDVLP KQIKSVLLDT 480 AGFHDVM*

Sequence ? help Back to Top

Protein Sequence Length: 488 aa Download sequence Send to blast

MVLEPNGAVW MEGEEEQPLS VSWTTAAAAT ATTTARATTE PKEDEMHVNA VSLSGFKSIL  60
DTDWFLNSTL NNPPQDFTNT TGLLETHQEL RAFNAFQETN LFFQPIESHP FTLNPTHSLL  120
PPNNNDNNSN SHLPFVSGFD LGGEAAGFIQ PASGFMGLTT TQICATNDSD FHGFGSSYSN  180
CFDNLEGLFF NSNSKAKVCS QSQPTLFEKR AALRQSSGKL ENLEILGGNL LLENIKCRKN  240
EEASVDISSL NYESDEYNNN NNNNNASNDN NVNGKVDESV KNWNAGGSAT VGDNKGKRKG  300
LPAKNLMAER RRRKKLNDRL YMLRSVVPKI SKMDRASILG DAIDYLKELL QRINDLHNEL  360
ESTPTGSLMQ PSTSIQPMTP TPPTLPCRVK EEISRSPTGE AARVEVRIRE GRAVNIHMFC  420
ARRPGLLLST MRALDSLGLD IQQAVISCFN GFALDVFRAE QCREGQDVLP KQIKSVLLDT  480
AGFHDVM*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	296	314	KRKGLPAKNLMAERRRRKK
2	308	315	ERRRRKKL

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.10399	0.0	callus\| fruit
Csi.5246	0.0	callus

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Widely expressed in the whole plant with high expression in leaves and stem. Broad expression within stomatal cell lineages of leaf epidermis. {ECO:0000269\|PubMed:18641265}.

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	JX512645	0.0	JX512645.1 Citrus trifoliata bHLH mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006446948.1	0.0	transcription factor ICE1
Refseq	XP_006446949.1	0.0	transcription factor ICE1
Refseq	XP_006468882.1	0.0	transcription factor ICE1
Swissprot	Q9LSE2	1e-121	ICE1_ARATH; Transcription factor ICE1
TrEMBL	A0A067DWI3	0.0	A0A067DWI3_CITSI; Uncharacterized protein
TrEMBL	V4W2Q3	0.0	V4W2Q3_9ROSI; Uncharacterized protein
STRING	XP_006468882.1	0.0	(Citrus sinensis)
STRING	XP_006446948.1	0.0	(Citrus clementina)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G26744.4	1e-109	bHLH family protein

Link Out ? help Back to Top
Phytozome	orange1.1g011398m
Entrez Gene	102620321

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]