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

898955

Common Name

ARALYDRAFT_898955

Organism

Arabidopsis lyrata

Taxonomic ID

81972

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: 401aa MW: 45020.2 Da PI: 5.3318

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
898955	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.1	2.8e-12	193	244	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++h ++Er+RR+++N+ + Lr+l+P + + ++ + a+i A+e++++L+ 898955 193 QRMTHIAVERNRRKQMNEHLRVLRSLMPGS---YVQRGDQASIIGGAIEFVRELE 244 79**************************...9***************9995 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	1.4E-13	191	247	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.09E-12	191	248	No hit	No description
SuperFamily	SSF47459	2.22E-16	192	257	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.428	192	243	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.3E-9	193	244	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.4E-9	198	249	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	0.00207	326	390	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: 401 aa Download sequence Send to blast
MDKDYSAPNF LGESSGGNDD NSSGMIDYMF NRNLQHQQKQ SMPQQQHHQL SPSGFGATPF 60 DKMNFSDVMQ FADFGPKLAL NQTRNQDDQE TGIDPVYFLK FPVLNDKIED HNQTQHLMPS 120 HQTSQEGGEC GGNIGNVFLE EKEDQDDDNN SVQLRFIGGE EEDRENKNVT TKEVKSKRKR 180 ARTSKTSEEV ESQRMTHIAV ERNRRKQMNE HLRVLRSLMP GSYVQRGDQA SIIGGAIEFV 240 RELEQLLQCL ESQKRRRILG ETGRDMTTTT TSSSSPITAV ANQTQPLIIT GNVTELEGGG 300 GLREETAENK SCLADVEVKL LGFDAMIKIL SRRRPGQLIK TIAALEDLHL SILHTNITTM 360 EQTVLYSFNV KITSETRFTA EDIASSIQQI FSFIHANTNM *

Sequence ? help Back to Top

Protein Sequence Length: 401 aa Download sequence Send to blast

MDKDYSAPNF LGESSGGNDD NSSGMIDYMF NRNLQHQQKQ SMPQQQHHQL SPSGFGATPF  60
DKMNFSDVMQ FADFGPKLAL NQTRNQDDQE TGIDPVYFLK FPVLNDKIED HNQTQHLMPS  120
HQTSQEGGEC GGNIGNVFLE EKEDQDDDNN SVQLRFIGGE EEDRENKNVT TKEVKSKRKR  180
ARTSKTSEEV ESQRMTHIAV ERNRRKQMNE HLRVLRSLMP GSYVQRGDQA SIIGGAIEFV  240
RELEQLLQCL ESQKRRRILG ETGRDMTTTT TSSSSPITAV ANQTQPLIIT GNVTELEGGG  300
GLREETAENK SCLADVEVKL LGFDAMIKIL SRRRPGQLIK TIAALEDLHL SILHTNITTM  360
EQTVLYSFNV KITSETRFTA EDIASSIQQI FSFIHANTNM *

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	193	204	RMTHIAVERNRR
2	253	257	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	898955

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK221324	0.0	AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBank	BT028961	0.0	BT028961.1 Arabidopsis thaliana At3g24140 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002883481.2	0.0	transcription factor FAMA
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	D7L481	0.0	D7L481_ARALL; Uncharacterized protein
STRING	scaffold_302925.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5548	26	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24140.1	0.0	bHLH family protein

Link Out ? help Back to Top
Phytozome	898955
Entrez Gene	9319548

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] 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]