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_00169.1_g00004.1

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: 401aa MW: 45194.4 Da PI: 4.7506

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00169.1_g00004.1	genome	RGD	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	194	245	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++h ++Er+RR+++N+ + Lr+l+P + + ++ + a+i A+e++++L+ Rsa1.0_00169.1_g00004.1 194 QRMTHIAVERNRRKQMNEHLRVLRSLMPGS---YVQRGDQASIIGGAIEFVRELE 245 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	192	248	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.40E-12	192	249	No hit	No description
SuperFamily	SSF47459	2.49E-16	193	258	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.428	193	244	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.3E-9	194	245	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.4E-9	199	250	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	0.00131	327	391	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
MAMDKEYSAP NFLGESSGGK DDTSDGMIDY MFNRNLQQEK QSMPQQHQLS PSGFGATPTF 60 DKMSFADVMQ FADFGPKLAL NQTRNQDDQD TGQGMDPVYF LKFPVLNDKI EDHNQTHYLM 120 SQEAGECEGN IGNLFLEEKE NQEDENDNNS VQLRFIGGEE EEDDRENKNV TTKEVKSKRK 180 RARTSKTSEE VESQRMTHIA VERNRRKQMN EHLRVLRSLM PGSYVQRGDQ ASIIGGAIEF 240 VRELEQLLQC LESQKRRRIL GETGNRHLGD MTTTTTTSSP ITSVNNPLII TGNVTESEGG 300 GGLQEETAEN KSCLADVEVK LLGFDAMIKI LSRRRPGQLI KTIAALEDLH LSILHTNITT 360 MEQTVLYSFN VKITSETRFT AEDIASSIQE IFTFIHANTT M

Sequence ? help Back to Top

Protein Sequence Length: 401 aa Download sequence Send to blast

MAMDKEYSAP NFLGESSGGK DDTSDGMIDY MFNRNLQQEK QSMPQQHQLS PSGFGATPTF  60
DKMSFADVMQ FADFGPKLAL NQTRNQDDQD TGQGMDPVYF LKFPVLNDKI EDHNQTHYLM  120
SQEAGECEGN IGNLFLEEKE NQEDENDNNS VQLRFIGGEE EEDDRENKNV TTKEVKSKRK  180
RARTSKTSEE VESQRMTHIA VERNRRKQMN EHLRVLRSLM PGSYVQRGDQ ASIIGGAIEF  240
VRELEQLLQC LESQKRRRIL GETGNRHLGD MTTTTTTSSP ITSVNNPLII TGNVTESEGG  300
GGLQEETAEN KSCLADVEVK LLGFDAMIKI LSRRRPGQLI KTIAALEDLH LSILHTNITT  360
MEQTVLYSFN VKITSETRFT AEDIASSIQE IFTFIHANTT M

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	194	205	RMTHIAVERNRR
2	254	258	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	Rsa1.0_00169.1_g00004.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB493631	1e-120	AB493631.1 Arabidopsis thaliana At3g24140 mRNA for hypothetical protein, partial cds, clone: RAAt3g24140.
GenBank	AF488624	1e-120	AF488624.1 Arabidopsis thaliana clone bHLH097 putative bHLH transcription factor mRNA, partial sequence.
GenBank	AK221324	1e-120	AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBank	BT028961	1e-120	BT028961.1 Arabidopsis thaliana At3g24140 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018434615.1	0.0	PREDICTED: transcription factor FAMA-like
Refseq	XP_018434616.1	0.0	PREDICTED: transcription factor FAMA-like
Refseq	XP_018434618.1	0.0	PREDICTED: transcription factor FAMA-like
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	M4EHU2	0.0	M4EHU2_BRARP; Uncharacterized protein
STRING	Bra028357.1-P	0.0	(Brassica rapa)

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

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]