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

AT1G12860.1

Common Name

BHLH33, EN44, F13K23.12, ICE2, SCRM2

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 450aa MW: 49795.7 Da PI: 6.1898

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G12860.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	36	1.2e-11	270	312	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL A++Y+k+L AT1G12860.1 270 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIDYLKEL 312 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	263	312	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	5.63E-17	266	337	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.9E-9	269	312	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-14	269	318	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.54E-13	270	316	No hit	No description
Gene3D	G3DSA:4.10.280.10	7.6E-16	270	327	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS51671	8.734	378	450	IPR002912	ACT domain
CDD	cd04873	8.58E-7	379	420	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010444	Biological Process	guard mother cell differentiation
GO:0050826	Biological Process	response to freezing
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0016597	Molecular Function	amino acid binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 450 aa Download sequence Send to blast
MNSDGVWLDG SGESPEVNNG EAASWVRNPD EDWFNNPPPP QHTNQNDFRF NGGFPLNPSE 60 NLLLLLQQSI DSSSSSSPLL HPFTLDAASQ QQQQQQQQQE QSFLATKACI VSLLNVPTIN 120 NNTFDDFGFD SGFLGQQFHG NHQSPNSMNF TGLNHSVPDF LPAPENSSGS CGLSPLFSNR 180 AKVLKPLQVM ASSGSQPTLF QKRAAMRQSS SSKMCNSESS SEMRKSSYER EIDDTSTGII 240 DISGLNYESD DHNTNNNKGK KKGMPAKNLM AERRRRKKLN DRLYMLRSVV PKISKMDRAS 300 ILGDAIDYLK ELLQRINDLH TELESTPPSS SSLHPLTPTP QTLSYRVKEE LCPSSSLPSP 360 KGQQPRVEVR LREGKAVNIH MFCGRRPGLL LSTMRALDNL GLDVQQAVIS CFNGFALDVF 420 RAEQCQEDHD VLPEQIKAVL LDTAGYAGLV

Sequence ? help Back to Top

Protein Sequence Length: 450 aa Download sequence Send to blast

MNSDGVWLDG SGESPEVNNG EAASWVRNPD EDWFNNPPPP QHTNQNDFRF NGGFPLNPSE  60
NLLLLLQQSI DSSSSSSPLL HPFTLDAASQ QQQQQQQQQE QSFLATKACI VSLLNVPTIN  120
NNTFDDFGFD SGFLGQQFHG NHQSPNSMNF TGLNHSVPDF LPAPENSSGS CGLSPLFSNR  180
AKVLKPLQVM ASSGSQPTLF QKRAAMRQSS SSKMCNSESS SEMRKSSYER EIDDTSTGII  240
DISGLNYESD DHNTNNNKGK KKGMPAKNLM AERRRRKKLN DRLYMLRSVV PKISKMDRAS  300
ILGDAIDYLK ELLQRINDLH TELESTPPSS SSLHPLTPTP QTLSYRVKEE LCPSSSLPSP  360
KGQQPRVEVR LREGKAVNIH MFCGRRPGLL LSTMRALDNL GLDVQQAVIS CFNGFALDVF  420
RAEQCQEDHD VLPEQIKAVL LDTAGYAGLV

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	259	277	KKKGMPAKNLMAERRRRKK
2	271	278	ERRRRKKL

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.42057	0.0	floral meristem\| flower\| leaf\| seed\| vegetative tissue

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	334182534	0.0
Genevisible	261196_at	0.0
Expression Atlas	AT1G12860	-
AtGenExpress	AT1G12860	-
ATTED-II	AT1G12860	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. Broad expression within stomatal cell lineages of leaf epidermis, except in mature guard-cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:18641265}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes ICE2 (Inducer of CBF Expression 2), a transcription factor of the bHLH family that participates in the response to deep freezing through the cold acclimation-dependent pathway. Overexpression of ICE2 results in increased tolerance to deep freezing stress after cold acclimation.
UniProt	Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA (PubMed:18641265). Functions as a dimer with SPCH during stomatal initiation (PubMed:18641265, PubMed:28507175). {ECO:0000269\|PubMed:18641265, ECO:0000269\|PubMed:28507175}.

Function -- GeneRIF ? help Back to Top
These results suggested that the CBF1 transcription factor, known as one of the regulators of the cold stress response, has a dominant role in providing freezing tolerance in transgenic plants characterized by overexpression of ICE2. [PMID: 19026725] Jasmonate functions as a critical upstream signal of the ICE-CBF/DREB1 pathway to positively regulate Arabidopsis freezing tolerance. [PMID: 23933884] ICE2 gene has originated from a duplication event about 17.9MYA followed by sub- and neofunctionalization of the ancestral ICE1 gene. [PMID: 25443829] unified ICE-CBF pathway provides transcriptional feedback control of freezing tolerance during cold acclimation [PMID: 26311645]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G12860.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT5G53210(A)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9LPW3

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G12860

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK118011	0.0	AK118011.1 Arabidopsis thaliana At1g12860 mRNA for putative bHLH transcription factor (bHLH033), complete cds, clone: RAFL19-21-N13.
GenBank	BT005377	0.0	BT005377.1 Arabidopsis thaliana At1g12860 mRNA, complete cds.
GenBank	EU369670	0.0	EU369670.1 Arabidopsis thaliana bHLH protein (SCREAM2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_172746.2	0.0	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Swissprot	Q9LPW3	0.0	SCRM2_ARATH; Transcription factor SCREAM2
TrEMBL	A0A1P8AMV9	0.0	A0A1P8AMV9_ARATH; Basic helix-loop-helix (BHLH) DNA-binding superfamily protein
STRING	AT1G12860.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1952	27	82
Representative plant	OGRP557	16	78

Link Out ? help Back to Top
Phytozome	AT1G12860.1
Entrez Gene	837843
iHOP	AT1G12860
wikigenes	AT1G12860

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Chinnusamy V, et al. ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev., 2003. 17(8): p. 1043-54 [PMID:12672693] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Nawy T, et al. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell, 2005. 17(7): p. 1908-25 [PMID:15937229] Kanaoka MM, et al. SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation. Plant Cell, 2008. 20(7): p. 1775-85 [PMID:18641265] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Fursova OV,Pogorelko GV,Tarasov VA Identification of ICE2, a gene involved in cold acclimation which determines freezing tolerance in Arabidopsis thaliana. Gene, 2009. 429(1-2): p. 98-103 [PMID:19026725] Tarasov VA,Khadeeva NV,Mel'nik VA,Ezhova TA,Shestakov SV The Atlg12860 gene of Arabidopsis thaliana determines cathelicidin-like antimicrobial activity. Dokl. Biol. Sci., 2009. [PMID:19760875] Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Hanada K, et al. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol. Biol. Evol., 2011. 28(1): p. 377-82 [PMID:20736450] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Hu Y,Jiang L,Wang F,Yu D Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis. Plant Cell, 2013. 25(8): p. 2907-24 [PMID:23933884] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Kurbidaeva A,Ezhova T,Novokreshchenova M Arabidopsis thaliana ICE2 gene: phylogeny, structural evolution and functional diversification from ICE1. Plant Sci., 2014. 229: p. 10-22 [PMID:25443829] Emmerstorfer A, et al. Over-expression of ICE2 stabilizes cytochrome P450 reductase in Saccharomyces cerevisiae and Pichia pastoris. Biotechnol J, 2015. 10(4): p. 623-35 [PMID:25641738] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] 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] Kim YS,Lee M,Lee JH,Lee HJ,Park CM The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis. Plant Mol. Biol., 2015. 89(1-2): p. 187-201 [PMID:26311645] Raissig MT,Abrash E,Bettadapur A,Vogel JP,Bergmann DC Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(29): p. 8326-31 [PMID:27382177] Fu ZW,Wang YL,Lu YT,Yuan TT Nitric oxide is involved in stomatal development by modulating the expression of stomatal regulator genes in Arabidopsis. Plant Sci., 2016. 252: p. 282-289 [PMID:27717464] 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]