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

Rsa1.0_28455.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 182aa MW: 20933.2 Da PI: 5.1673

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_28455.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	28.7	2.4e-09	149	177	1	29
CHHHHHHHHHHHHHHHHHHHHHHHCTSCC CS HLH 1 rrrahnerErrRRdriNsafeeLrellPk 29 +r++h ++Er+RR+++N+ + Lr+l+P Rsa1.0_28455.1_g00001.1 149 QRMTHIAVERNRRKQMNEHLRVLRSLMPG 177 79**************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.47E-8	140	179	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.2E-8	147	178	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.43E-7	147	182	No hit	No description
PROSITE profile	PS50888	11.82	148	182	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.0E-6	149	177	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

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: 182 aa Download sequence Send to blast
MPQQHQLSPS GFGATPAFDK MSFADVMQFA DFGPKLALNQ TGNQENQETG MDPVYFLKFP 60 VLNDKIEDHN QTHNLMSQEG GECEGNIGNV FLEEKENQDV ENDNNSVQLR FIGGEEEEER 120 ENKNDTTKEV KSKRKRARTS KTSEEVESQR MTHIAVERNR RKQMNEHLRV LRSLMPGSYV 180 QR

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	149	160	RMTHIAVERNRR

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	Rsa1.0_28455.1_g00001.1

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_018485826.1	1e-132	PREDICTED: transcription factor FAMA-like isoform X4
Swissprot	Q56YJ8	1e-100	FAMA_ARATH; Transcription factor FAMA
TrEMBL	A0A3P5ZZI0	1e-116	A0A3P5ZZI0_BRACM; Uncharacterized protein
TrEMBL	V4L0U0	1e-116	V4L0U0_EUTSA; Uncharacterized protein
STRING	XP_006418807.1	1e-116	(Eutrema salsugineum)

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	2e-86	bHLH family protein

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]