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

XP_013631585.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 400aa MW: 45428.9 Da PI: 8.5869

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013631585.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.5	1.8e-11	189	240	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++ ++Er+RR+++N+ + Lr+l+P + + k+ +Ka+i ++e++++L+ XP_013631585.1 189 QRMTRIMVERKRRKQMNEHLRVLRSLMPGS---YVKRGDKASIIGGVIEFVRELE 240 69999***********************...9***************9985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	7.95E-10	187	237	No hit	No description
Gene3D	G3DSA:4.10.280.10	3.6E-12	187	241	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	7.07E-15	188	256	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.046	188	239	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	8.5E-9	189	240	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.5E-9	194	245	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	2.84E-5	326	390	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: 400 aa Download sequence Send to blast
MDKYYSASNF FGKPLGGHDS NSSGMIDYTL NGDLQPQKQP MLQQQPHQLS PSEFGATPFF 60 DKKTFIDMMH FADFGPKLAL NRTNNQAVQE TGFDPVCFLK FPVLKERIED HIRTQHLMSS 120 HRTPQEGGEC GGNIGCVFLE DQDNNSRRLR FIRGGENEDR DNNNVTTKEV NSKRKRARTS 180 KTIEEVESQR MTRIMVERKR RKQMNEHLRV LRSLMPGSYV KRGDKASIIG GVIEFVRELE 240 ELLPCLESQK RRRILEETGH RQTRGMTRPT NPSSCPVTRV ANQTQPLIIT KNITELEGGG 300 GLLEEMTENK SCLADVEVKL LGFDAMIKIL SKRRPGQLLM TMAALEDLHL SILHTSITTM 360 EQTVLYSFIV KITSETKFTA EDIASSIQQI FSFIHGSTIM

Sequence ? help Back to Top

Protein Sequence Length: 400 aa Download sequence Send to blast

MDKYYSASNF FGKPLGGHDS NSSGMIDYTL NGDLQPQKQP MLQQQPHQLS PSEFGATPFF  60
DKKTFIDMMH FADFGPKLAL NRTNNQAVQE TGFDPVCFLK FPVLKERIED HIRTQHLMSS  120
HRTPQEGGEC GGNIGCVFLE DQDNNSRRLR FIRGGENEDR DNNNVTTKEV NSKRKRARTS  180
KTIEEVESQR MTRIMVERKR RKQMNEHLRV LRSLMPGSYV KRGDKASIIG GVIEFVRELE  240
ELLPCLESQK RRRILEETGH RQTRGMTRPT NPSSCPVTRV ANQTQPLIIT KNITELEGGG  300
GLLEEMTENK SCLADVEVKL LGFDAMIKIL SKRRPGQLLM TMAALEDLHL SILHTSITTM  360
EQTVLYSFIV KITSETKFTA EDIASSIQQI FSFIHGSTIM

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	249	253	KRRRI

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Not expressed in meristemoids, but strongly expressed in guard mother cells (GMCs) and in young guard cells (at protein level) (PubMed:17088607). Expressed at the transition to terminal stomatal differentiation, just before and after the symmetric division of stomatal differentiation, being confined to late-stage GMC and to young, still differentiating guard cells (PubMed:24571519). {ECO:0000269\|PubMed:17088607, ECO:0000269\|PubMed:24571519}.
Uniprot	TISSUE SPECIFICITY: Resctricted to stomatal cell lineages (at protein level). Expressed in roots, leaves, stems, and flowers. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:17088607}.

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	XP_013631585.1

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_013631585.1	0.0	PREDICTED: transcription factor FAMA-like
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	A0A0D3AB07	0.0	A0A0D3AB07_BRAOL; Uncharacterized protein
STRING	Bo1g101200.1	0.0	(Brassica oleracea)

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-180	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]