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

evm_27.model.AmTr_v1.0_scaffold00089.12

Common Name

AMTR_s00089p00043950, LOC18429905

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

bHLH

Protein Properties

Length: 331aa MW: 36482 Da PI: 5.095

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00089.12	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	39.5	1e-12	142	193	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++h ++Er+RR+++N+ + Lr+l+P + + ++ + a+i A+e++++L+ evm_27.model.AmTr_v1.0_scaffold00089.12 142 QRMTHIAVERNRRKQMNEHLRVLRSLMPAS---YVQRGDQASIIGGAIEFVRELE 193 79**************************...9***************9995 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	3.93E-12	140	197	No hit	No description
SuperFamily	SSF47459	1.83E-16	141	206	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	7.4E-14	141	196	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.135	141	192	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	4.4E-10	142	193	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.9E-9	147	198	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	2.94E-4	257	321	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010377	Biological Process	guard cell fate commitment
GO:0045597	Biological Process	positive regulation of cell differentiation
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0051782	Biological Process	negative regulation of cell division
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 331 aa Download sequence Send to blast
MDKDEASYSV MMQGNYSGID NSGAIPEYSM NGGLCTWASL ERLGFGEHAG VDSEMGIEFL 60 KFPVLSERFE HEGVMNSSKT IEEEEIEEEE RETGSHGAIN SSKNSRNESV GVANSGGGEM 120 EQGKGRRKRG RSMKTSEEVE NQRMTHIAVE RNRRKQMNEH LRVLRSLMPA SYVQRGDQAS 180 IIGGAIEFVR ELEQLLQCLE SQKRRRILGG AEGQGGGLVV MGGVEGQQQQ MAVEEEGAER 240 RSCVADIEVR VAGGDAMIKV LSRRRPGQLL RTIAALEEMP LSILHTNITT IDHTVLYSFN 300 VKIIGDSRFT AEDIASSVQQ IFNFIHANTI *

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	142	153	RMTHIAVERNRR
2	202	206	KRRRI

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator (PubMed:17088607, PubMed:17183265, PubMed:17183267). Together with MYB88 and MYB124, ensures that stomata contain just two guard cells (GCs) by enforcing a single symmetric precursor cell division before stomatal maturity (PubMed:24571519). Together with SPCH and MUTE, regulates the stomata formation. Required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Mediates the formation of stomata (PubMed:17088607, PubMed:17183265, PubMed:17183267). Prevents histone H3K27me3 marks and derepresses stem cell gene expression (PubMed:24654956). {ECO:0000269\|PubMed:17088607, ECO:0000269\|PubMed:17183265, ECO:0000269\|PubMed:17183267, ECO:0000269\|PubMed:24571519, ECO:0000269\|PubMed:24654956}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Inhibited by low relative humidity (LRH) via epigenetic CG methylation, thus leading to a reduced stomatal index. {ECO:0000269\|PubMed:22442411}.

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_006840140.1	0.0	transcription factor FAMA
Swissprot	Q56YJ8	1e-103	FAMA_ARATH; Transcription factor FAMA
TrEMBL	W1P4D2	0.0	W1P4D2_AMBTC; Uncharacterized protein
STRING	ERN01815	0.0	(Amborella trichopoda)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP253	15	131

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24140.1	3e-78	bHLH family protein

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00089.12
Entrez Gene	18429905

Publications ? help Back to Top
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] Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323] Matos JL, et al. Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module. Elife, 2015. [PMID:25303364] 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] 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] Han X, et al. Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons. Plant Physiol., 2018. 176(4): p. 2871-2885 [PMID:29496884] Li X,Yang R,Chen H The Arabidopsis thaliana Mediator subunit MED8 regulates plant immunity to Botrytis Cinerea through interacting with the basic helix-loop-helix (bHLH) transcription factor FAMA. PLoS ONE, 2018. 13(3): p. e0193458 [PMID:29513733]