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_009107621.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 427aa MW: 48331.2 Da PI: 7.2998

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009107621.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	31.7	2.7e-10	216	267	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++ ++Er+RR+++N+ + Lr+l+P + + k+ + a+i ++e++++L+ XP_009107621.1 216 QRMTRIMVERKRRKQMNEHLRVLRSLMPGS---YVKRGDQASIIGGVIEFVRELE 267 69999***********************...9***************9985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	3.9E-11	214	268	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.33E-9	214	264	No hit	No description
PROSITE profile	PS50888	14.488	215	266	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	3.53E-14	215	282	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.4E-7	216	267	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	5.8E-8	221	272	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	3.14E-5	353	417	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: 427 aa Download sequence Send to blast
MVSEPDPYNP IRSIIDPAQS RPIDPCPNIP RLTLKEPSSR GGLNNDSNSS GMIDYTLNGD 60 LQPQKQPMLQ QQPHQLSPSE FGATPFFDKK IFIDIMHFAD FGPKLALNRT NNQAVHETGF 120 DPVCFLKFPV LKERIEDHIR TQHLMSSHRT PQEGGECGGN IGCVFLEDQD NNSRRLRFIR 180 GGENEDRDND NVTTKEVNSK RKRGRTSKTI EEVESQRMTR IMVERKRRKQ MNEHLRVLRS 240 LMPGSYVKRG DQASIIGGVI EFVRELEELL PCLESQKRRR ILEETGHRQT GDMTRPTNPS 300 SCPVTRVANQ TQPLIITKNI TELEGGGGLL EEMTENKSCL ADVEVKLLGF DAMIKILSKR 360 RPGQLLMTMA ALEDLHLSIL HTSITTMEQT VLYSFIVKIT SETKFTAEDI ASSIQQIFSF 420 IHGCTIM

Sequence ? help Back to Top

Protein Sequence Length: 427 aa Download sequence Send to blast

MVSEPDPYNP IRSIIDPAQS RPIDPCPNIP RLTLKEPSSR GGLNNDSNSS GMIDYTLNGD  60
LQPQKQPMLQ QQPHQLSPSE FGATPFFDKK IFIDIMHFAD FGPKLALNRT NNQAVHETGF  120
DPVCFLKFPV LKERIEDHIR TQHLMSSHRT PQEGGECGGN IGCVFLEDQD NNSRRLRFIR  180
GGENEDRDND NVTTKEVNSK RKRGRTSKTI EEVESQRMTR IMVERKRRKQ MNEHLRVLRS  240
LMPGSYVKRG DQASIIGGVI EFVRELEELL PCLESQKRRR ILEETGHRQT GDMTRPTNPS  300
SCPVTRVANQ TQPLIITKNI TELEGGGGLL EEMTENKSCL ADVEVKLLGF DAMIKILSKR  360
RPGQLLMTMA ALEDLHLSIL HTSITTMEQT VLYSFIVKIT SETKFTAEDI ASSIQQIFSF  420
IHGCTIM

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	276	280	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_009107621.1

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_009107621.1	0.0	PREDICTED: transcription factor FAMA-like
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	A0A398ASI9	0.0	A0A398ASI9_BRACM; Uncharacterized protein
STRING	Bra028351.1-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-171	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]