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_009135876.1

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: 373aa MW: 42071.2 Da PI: 5.2148

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009135876.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.2	2.5e-12	165	216	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +r++h ++Er+RR+++N+ + Lr+l+P + + ++ + a+i A+e++++L+ XP_009135876.1 165 QRMTHIAVERNRRKQMNEHLRVLRSLMPGS---YVQRGDQASIIGGAIEFVRELE 216 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	1.2E-13	163	219	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.12E-12	163	220	No hit	No description
PROSITE profile	PS50888	15.428	164	215	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.96E-16	164	229	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.1E-9	165	216	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.4E-9	170	221	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	0.00185	299	363	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: 373 aa Download sequence Send to blast
MIDYMFNRNL QQQKQSMPQQ HQLSPSGFGA TTPTFDKMSF ADVMQFADFG PKLALNQTRN 60 QDDQETGLDP VYFLKFPVLN DKIEDHNQTH NLMSQEGGEC EGNIGNVFLE EKENQEDEND 120 NNSVQLRFIG GEEGDRENKN DTTKEVKSKR KRARTSKTSE EVESQRMTHI AVERNRRKQM 180 NEHLRVLRSL MPGSYVQRGD QASIIGGAIE FVRELEQLLQ CLESQKRRRI LGETGNRQIG 240 DMTTTMTSSS PITSVANPLI STGNVTELEG GGGGIREETA ENKSCLADVE VKLLGFDAMI 300 KILSRRRPGQ LIKTIAALED LHLSILHTNI TTMEQTVLYS FNVKITSETR FTAEDIASSI 360 QEIFSFIHAN TTM

Sequence ? help Back to Top

Protein Sequence Length: 373 aa Download sequence Send to blast

MIDYMFNRNL QQQKQSMPQQ HQLSPSGFGA TTPTFDKMSF ADVMQFADFG PKLALNQTRN  60
QDDQETGLDP VYFLKFPVLN DKIEDHNQTH NLMSQEGGEC EGNIGNVFLE EKENQEDEND  120
NNSVQLRFIG GEEGDRENKN DTTKEVKSKR KRARTSKTSE EVESQRMTHI AVERNRRKQM  180
NEHLRVLRSL MPGSYVQRGD QASIIGGAIE FVRELEQLLQ CLESQKRRRI LGETGNRQIG  240
DMTTTMTSSS PITSVANPLI STGNVTELEG GGGGIREETA ENKSCLADVE VKLLGFDAMI  300
KILSRRRPGQ LIKTIAALED LHLSILHTNI TTMEQTVLYS FNVKITSETR FTAEDIASSI  360
QEIFSFIHAN TTM

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	165	176	RMTHIAVERNRR
2	225	229	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_009135876.1

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	AK221324	0.0	AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBank	BT028961	0.0	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)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24140.1	1e-175	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]