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_009102547.1

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: 390aa MW: 44279.8 Da PI: 5.4856

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009102547.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	36.6	8.1e-12	184	235	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r ah ++Er+RR+++N+ + Lr+l+P + + ++ + a+i+ ++e++++L+ XP_009102547.1 184 QRLAHIAVERNRRKQMNEHLCVLRSLMPGS---YVQRRDQASIVGGVIEFLSELE 235 699*************************...9***************9985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	5.83E-12	182	239	No hit	No description
Gene3D	G3DSA:4.10.280.10	2.0E-11	182	238	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	5.63E-15	183	247	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	14.259	183	234	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.7E-9	184	235	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.2E-7	189	240	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: 390 aa Download sequence Send to blast
MDKDYPAPNF LSEYSCSNDD NSSGMIDHMF KRNLQKQKQS MPQQQQLSPS GFGATPTFDK 60 MSFADVMQFA DFGPMLALNQ TRSQNDQETW MDPFYILKFP VFNGDHNQTH HIMSQEGGGC 120 EGNISNVFLE EQDNQEEKND KNSMQLRFIG EEEDRENKND TTKEVKKKRK RARTSKTSEE 180 VESQRLAHIA VERNRRKQMN EHLCVLRSLM PGSYVQRRDQ ASIVGGVIEF LSELEQLLQC 240 LESQKRRRIL GETNDIHGGD MTTTVITSSA ITSSNPLIIT GNVTELEGGG GIQEETAEKK 300 SCLADVEVKL LGFNAMIKIL SRRRPRQLIM TIAALEDLHL SILHTNITTM EQTVLYSFNV 360 KITSETRFTA EDIASSIQEI YSFIHANSTM

Sequence ? help Back to Top

Protein Sequence Length: 390 aa Download sequence Send to blast

MDKDYPAPNF LSEYSCSNDD NSSGMIDHMF KRNLQKQKQS MPQQQQLSPS GFGATPTFDK  60
MSFADVMQFA DFGPMLALNQ TRSQNDQETW MDPFYILKFP VFNGDHNQTH HIMSQEGGGC  120
EGNISNVFLE EQDNQEEKND KNSMQLRFIG EEEDRENKND TTKEVKKKRK RARTSKTSEE  180
VESQRLAHIA VERNRRKQMN EHLCVLRSLM PGSYVQRRDQ ASIVGGVIEF LSELEQLLQC  240
LESQKRRRIL GETNDIHGGD MTTTVITSSA ITSSNPLIIT GNVTELEGGG GIQEETAEKK  300
SCLADVEVKL LGFNAMIKIL SRRRPRQLIM TIAALEDLHL SILHTNITTM EQTVLYSFNV  360
KITSETRFTA EDIASSIQEI YSFIHANSTM

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	244	248	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_009102547.1

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_009102547.1	0.0	PREDICTED: transcription factor FAMA
Refseq	XP_013752047.1	0.0	transcription factor FAMA-like
Swissprot	Q56YJ8	0.0	FAMA_ARATH; Transcription factor FAMA
TrEMBL	A0A3P6AZX7	0.0	A0A3P6AZX7_BRACM; Uncharacterized protein
STRING	Bo7g037540.1	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]