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

RrC9504_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 369aa MW: 41529.5 Da PI: 5.0026

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC9504_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.3	2.5e-12	164	215	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++h ++Er+RR+++N+ + Lr+l+P + + ++ + a+i A+e++++L+ RrC9504_p1 164 QRMTHIAVERNRRKQMNEHLRVLRSLMPGS---YVQRGDQASIIGGAIEFVRELE 215 79**************************...9***************9995 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.36E-12	162	219	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.2E-13	162	218	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.09E-16	163	228	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.428	163	214	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.1E-9	164	215	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.4E-9	169	220	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	0.00661	298	360	No hit	No description

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: 369 aa Download sequence Send to blast
MIDYMFNRNL QQQKQSMPQQ HQLSPSGFGA TPAFDKMSFA DVMQFADFGP KLALNQTGNQ 60 DNQETGMDPV YFLKFPVLND KIEDHNQTHN LMSQEGGECE GNIGNVFLEE KENQDVENDN 120 NSVQLRFIGG EEEERENKND TTKEVKSKRK RARTSKTSEE VESQRMTHIA VERNRRKQMN 180 EHLRVLRSLM PGSYVQRGDQ ASIIGGAIEF VRELEQLLQC LESQKRRRIL GDTGNRQIGD 240 MTTTMTSSSP ITSVVNPLTS TGNVTELEGG GGGLQEETAE NKSCLADVEV KLLGFDAMIK 300 ILSRRRPGQL IKTIAALEDL HLSILHTNIT TMEQTVLYSF NITSETRFTA EDIASSIQEI 360 FSFIHANTT

Sequence ? help Back to Top

Protein Sequence Length: 369 aa Download sequence Send to blast

MIDYMFNRNL QQQKQSMPQQ HQLSPSGFGA TPAFDKMSFA DVMQFADFGP KLALNQTGNQ  60
DNQETGMDPV YFLKFPVLND KIEDHNQTHN LMSQEGGECE GNIGNVFLEE KENQDVENDN  120
NSVQLRFIGG EEEERENKND TTKEVKSKRK RARTSKTSEE VESQRMTHIA VERNRRKQMN  180
EHLRVLRSLM PGSYVQRGDQ ASIIGGAIEF VRELEQLLQC LESQKRRRIL GDTGNRQIGD  240
MTTTMTSSSP ITSVVNPLTS TGNVTELEGG GGGLQEETAE NKSCLADVEV KLLGFDAMIK  300
ILSRRRPGQL IKTIAALEDL HLSILHTNIT TMEQTVLYSF NITSETRFTA EDIASSIQEI  360
FSFIHANTT

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	164	175	RMTHIAVERNRR
2	224	228	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB493631	3e-99	AB493631.1 Arabidopsis thaliana At3g24140 mRNA for hypothetical protein, partial cds, clone: RAAt3g24140.
GenBank	AF488624	3e-99	AF488624.1 Arabidopsis thaliana clone bHLH097 putative bHLH transcription factor mRNA, partial sequence.
GenBank	AK221324	3e-99	AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBank	BT028961	3e-99	BT028961.1 Arabidopsis thaliana At3g24140 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009135876.1	0.0	PREDICTED: transcription factor FAMA isoform X2
Refseq	XP_013685447.1	0.0	transcription factor FAMA isoform X2
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	A0A398A5T5	0.0	A0A398A5T5_BRACM; Uncharacterized protein
STRING	Bra001929.1-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	1e-176	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]