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

Gorai.003G116300.1

Common Name

B456_003G116300, LOC105788636

Organism

Gossypium raimondii

Taxonomic ID

29730

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

bHLH

Protein Properties

Length: 555aa MW: 60768.6 Da PI: 5.5055

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.003G116300.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	36.3	9.8e-12	369	411	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL A+eY+k+L Gorai.003G116300.1 369 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIEYLKEL 411 79*******************66......**************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.58	362	411	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.2E-16	365	434	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.3E-9	368	411	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.2E-14	368	417	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.82E-12	369	415	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.4E-15	369	424	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	3.14E-4	483	524	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: 555 aa Download sequence Send to blast
MLPRVSGGVI WMEDKEDEDS ASWNRTSYNS SNNNNNNNSG VIMENKEDMG TFSTFKSMLD 60 DEWYVGNNSI SSHQDIRDLS FTSNLGDHHQ DNLLLHHHSL PSVDSSSSCS PSSSVFNHLD 120 PSQVQYFCQP KPNLSSILNF VSNSPLDHGF DLSEIGFLDN QATIGTTLLN RGNAGVLGSL 180 TDLGHDNHLD PANLCPEAQF SSSRIVQLPE NGTGFAGFEG FDENPGNALF LKRSKLLRPL 240 ESCPSVGAQP TLFQKRAAMR KNSADSGPNF GVLDGGKFSV SSGTEGDKGK KEMGKEENEK 300 RKINNRDDVE DVSIDESALN YDSDEFTENT KVEETLKNGG NTINANTNAT GGDQNQKGKR 360 KGLPAKNLMA ERRRRKKLND RLYMLRSVVP KISKMDRASI LGDAIEYLKE LLQRINDLHN 420 ELESTLPSSS LTPTTSSFHP LTPTPATFPS RIKDELGPSS SPGLNGQPAR VEVRLREGKA 480 VNIHMFCGRR PGLLLSIIRA LDNLGLDAQQ AVISCFNGFS MDIFRAEQCK EGQDINPGNI 540 KAVLLDSTGF PNMI*

Sequence ? help Back to Top

Protein Sequence Length: 555 aa Download sequence Send to blast

MLPRVSGGVI WMEDKEDEDS ASWNRTSYNS SNNNNNNNSG VIMENKEDMG TFSTFKSMLD  60
DEWYVGNNSI SSHQDIRDLS FTSNLGDHHQ DNLLLHHHSL PSVDSSSSCS PSSSVFNHLD  120
PSQVQYFCQP KPNLSSILNF VSNSPLDHGF DLSEIGFLDN QATIGTTLLN RGNAGVLGSL  180
TDLGHDNHLD PANLCPEAQF SSSRIVQLPE NGTGFAGFEG FDENPGNALF LKRSKLLRPL  240
ESCPSVGAQP TLFQKRAAMR KNSADSGPNF GVLDGGKFSV SSGTEGDKGK KEMGKEENEK  300
RKINNRDDVE DVSIDESALN YDSDEFTENT KVEETLKNGG NTINANTNAT GGDQNQKGKR  360
KGLPAKNLMA ERRRRKKLND RLYMLRSVVP KISKMDRASI LGDAIEYLKE LLQRINDLHN  420
ELESTLPSSS LTPTTSSFHP LTPTPATFPS RIKDELGPSS SPGLNGQPAR VEVRLREGKA  480
VNIHMFCGRR PGLLLSIIRA LDNLGLDAQQ AVISCFNGFS MDIFRAEQCK EGQDINPGNI  540
KAVLLDSTGF PNMI*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	358	376	KRKGLPAKNLMAERRRRKK
2	370	377	ERRRRKKL

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012471050.1	0.0	PREDICTED: transcription factor ICE1-like
Swissprot	Q9LSE2	1e-132	ICE1_ARATH; Transcription factor ICE1
TrEMBL	A0A0D2NZV6	0.0	A0A0D2NZV6_GOSRA; Uncharacterized protein
STRING	Gorai.003G116300.1	0.0	(Gossypium raimondii)

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	1e-109	bHLH family protein

Link Out ? help Back to Top
Phytozome	Gorai.003G116300.1
Entrez Gene	105788636

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]