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

Sopim06g068870.0.1

Organism

Solanum pimpinellifolium

Taxonomic ID

4084

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

bHLH

Protein Properties

Length: 532aa MW: 58337.1 Da PI: 5.2502

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopim06g068870.0.1	genome	CSHL	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	34.1	4.9e-11	343	385	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++P + K++ a+iL A+eY+k+L Sopim06g068870.0.1 343 MAERRRRKKLNDRLYMLRSVVPRiS------KMDRASILGDAIEYLKEL 385 79*******************66......**************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.491	336	385	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.7E-16	339	403	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.1E-8	342	385	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.2E-14	342	391	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	6.74E-13	343	389	No hit	No description
Gene3D	G3DSA:4.10.280.10	5.8E-16	343	399	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	1.02E-6	460	520	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: 532 aa Download sequence Send to blast
MLSRVNSMQV WDMEGKQEEE KEENFSNKEN TTNVELENKQ DMELGALSTF KSMLDGTDVD 60 WYHNNMQNHT ENICFTQNFT ELAENSMFLQ PVVPVDSSSS CSPSSVSVFN NLDPSQVHYL 120 LAQKAINNNP LDYSFNLGCE NGFLEAQGMG GLNKGGFLLA GGGFHDLSSQ NQMGNPNLNS 180 FTQYPSSHLP QNTTTTGFSP LGFVDGSANE NSLFLNRSKL LKPLDNFASN GAQPTLFQKR 240 AALRKNLANT TGGSLGDFGG EIGQNSMNGE NERKRKWGSG EELDDVSFDG CTLSYDSDDL 300 TENVTNKVDD TVKNGGNSSN ATSTVTCGNQ KGKKKGLPAK NLMAERRRRK KLNDRLYMLR 360 SVVPRISKMD RASILGDAIE YLKELLQKIN DLHNELESTP PSSSLTQTTS FYPLTPTGPA 420 LPGRIKEELY PSSFASPLSS PTGQPARVEV KAREGRAVNI HMFCSRRPGL LLSTMRALDN 480 LGLDIQQAVI SCFNGFALDI FRAEQCKEGQ DFHPDQIKAV LLDSAGCHGM I*

Sequence ? help Back to Top

Protein Sequence Length: 532 aa Download sequence Send to blast

MLSRVNSMQV WDMEGKQEEE KEENFSNKEN TTNVELENKQ DMELGALSTF KSMLDGTDVD  60
WYHNNMQNHT ENICFTQNFT ELAENSMFLQ PVVPVDSSSS CSPSSVSVFN NLDPSQVHYL  120
LAQKAINNNP LDYSFNLGCE NGFLEAQGMG GLNKGGFLLA GGGFHDLSSQ NQMGNPNLNS  180
FTQYPSSHLP QNTTTTGFSP LGFVDGSANE NSLFLNRSKL LKPLDNFASN GAQPTLFQKR  240
AALRKNLANT TGGSLGDFGG EIGQNSMNGE NERKRKWGSG EELDDVSFDG CTLSYDSDDL  300
TENVTNKVDD TVKNGGNSSN ATSTVTCGNQ KGKKKGLPAK NLMAERRRRK KLNDRLYMLR  360
SVVPRISKMD RASILGDAIE YLKELLQKIN DLHNELESTP PSSSLTQTTS FYPLTPTGPA  420
LPGRIKEELY PSSFASPLSS PTGQPARVEV KAREGRAVNI HMFCSRRPGL LLSTMRALDN  480
LGLDIQQAVI SCFNGFALDI FRAEQCKEGQ DFHPDQIKAV LLDSAGCHGM I*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5gnj_A	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_B	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_E	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_F	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_G	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_I	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_M	2e-13	338	395	6	63	Transcription factor MYC2
5gnj_N	2e-13	338	395	6	63	Transcription factor MYC2
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	332	350	KKKGLPAKNLMAERRRRKK
2	344	351	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JX625139	0.0	JX625139.1 Solanum lycopersicum inducer of CBF expression 1 (ICE1a) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001274718.1	0.0	transcription factor ICE1-like
Swissprot	Q9LSE2	1e-124	ICE1_ARATH; Transcription factor ICE1
TrEMBL	K4C861	0.0	K4C861_SOLLC; Inducer of CBF expression 1
STRING	Solyc06g068870.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2703	24	52

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G26744.4	1e-118	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]