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

GSBRNA2T00000001001

Common Name

GSBRNA2T00000001001

Organism

Brassica napus

Taxonomic ID

3708

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: 606aa MW: 67723.1 Da PI: 4.974

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00000001001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.5	2.1e-12	415	461	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 +h Er+ R+++N++f +Lr+++P+ + K +K++iL +++Y+++Lq GSBRNA2T00000001001 415 NHALSERKCREKLNDRFMTLRSIIPSiS------KIDKVSILDDTIDYLQELQ 461 79999*******************66......****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	5.7E-51	13	202	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	15.974	411	460	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	5.1E-17	415	482	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	6.9E-10	415	461	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.7E-16	415	478	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	6.84E-14	415	465	No hit	No description
SMART	SM00353	1.4E-14	417	466	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009957	Biological Process	epidermal cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 606 aa Download sequence Send to blast
MATGENRTVQ ENLKKHLAVS VRNIQWSYGI FWSISASQPG VLEWGDGYYN GDIKTRKTIQ 60 AVEVKADQLG LERSDQLREL YESLSVAESS ASGGSQVSRR ASATALSPED LTDTEWYYLV 120 CMSFVFNIGE GITGGALGNG EPIWLCNAHT ADSKVFTRSL LAKSASLLTV VCFPFLGGVL 180 EIGTTEHITE DFNVIQCVKT LFLEAHPYGT ISTRSDYQEI FDPLNSDKYI PTFGTEAFPT 240 TSTSVFEQEL EDHDSFINGG GASQVQSWQF VGEELNNCVH QPVNSSDCVS QTFVGGTTGR 300 VSCNPRKSRP QRLGQIQEQS NRLNMDDDVH YQGVISTIFK TTHQLVLGPQ FQNFDKRSSF 360 TRWRRLPLSA KTLGEKSQNM LKKIVFEVPR MHQKELLLPD TPEDNMFKVG DETGNHALSE 420 RKCREKLNDR FMTLRSIIPS ISKIDKVSIL DDTIDYLQEL QRRVQELESC REYTDTEMQM 480 PMKRKKPEDE DERASANCLN TKRKESDVNV GEDEPADTGY AGLTDNLRIG SFGNEVVIEL 540 RCAWREGILL EIMDVISHLN LDSHSVQSST GDGLLCLTVN CKHKGTNIAT AGMIQEALQR 600 VAWIC*

Sequence ? help Back to Top

Protein Sequence Length: 606 aa Download sequence Send to blast

MATGENRTVQ ENLKKHLAVS VRNIQWSYGI FWSISASQPG VLEWGDGYYN GDIKTRKTIQ  60
AVEVKADQLG LERSDQLREL YESLSVAESS ASGGSQVSRR ASATALSPED LTDTEWYYLV  120
CMSFVFNIGE GITGGALGNG EPIWLCNAHT ADSKVFTRSL LAKSASLLTV VCFPFLGGVL  180
EIGTTEHITE DFNVIQCVKT LFLEAHPYGT ISTRSDYQEI FDPLNSDKYI PTFGTEAFPT  240
TSTSVFEQEL EDHDSFINGG GASQVQSWQF VGEELNNCVH QPVNSSDCVS QTFVGGTTGR  300
VSCNPRKSRP QRLGQIQEQS NRLNMDDDVH YQGVISTIFK TTHQLVLGPQ FQNFDKRSSF  360
TRWRRLPLSA KTLGEKSQNM LKKIVFEVPR MHQKELLLPD TPEDNMFKVG DETGNHALSE  420
RKCREKLNDR FMTLRSIIPS ISKIDKVSIL DDTIDYLQEL QRRVQELESC REYTDTEMQM  480
PMKRKKPEDE DERASANCLN TKRKESDVNV GEDEPADTGY AGLTDNLRIG SFGNEVVIEL  540
RCAWREGILL EIMDVISHLN LDSHSVQSST GDGLLCLTVN CKHKGTNIAT AGMIQEALQR  600
VAWIC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rqw_A	4e-15	8	202	8	192	Transcription factor MYC3
4rqw_B	4e-15	8	202	8	192	Transcription factor MYC3
4rs9_A	4e-15	8	202	8	192	Transcription factor MYC3
4yz6_A	4e-15	8	202	8	192	Transcription factor MYC3
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Localized in trichome developing region of leaves, prior to trichome initiation. Levels increase in initiating and young trichome cells, but dropped in the pavement cells between trichomes. Disappears in mature trichomes. {ECO:0000269\|PubMed:12917293}.
Uniprot	TISSUE SPECIFICITY: Ubiquitous with higher levels in buds and flowers. Specifically localized in developing root hair cells. Expressed in epidermal root hair cells (trichoblasts) and moves to root hairless cells (atrichoblasts) by a cell-to-cell movement through plasmodesmata (at protein level). {ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15590742}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2. {ECO:0000269\|PubMed:12917293, ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15590742}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00000001001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. Negatively regulated by MYB66/WER, GL3 and BHLH2 in the developing non-hair cells, and positively regulated by CPC and TRY in the developing hair cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15590742}.

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	AK353217	0.0	AK353217.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-32-J06.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013688436.1	0.0	transcription factor EGL1
Refseq	XP_013688437.1	0.0	transcription factor EGL1
Swissprot	Q9CAD0	0.0	EGL1_ARATH; Transcription factor EGL1
TrEMBL	A0A078F5I3	0.0	A0A078F5I3_BRANA; BnaC09g12820D protein
STRING	Bo9g035460.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2592	28	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G63650.3	0.0	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] Liu Z,Shi MZ,Xie DY Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. Planta, 2014. 239(4): p. 765-81 [PMID:24370633] Nayidu NK, et al. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS ONE, 2014. 9(4): p. e95877 [PMID:24755905] Cheng Y, et al. Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases. Elife, 2018. [PMID:24771765] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Ranocha P,Francoz E,Burlat V,Dunand C Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Plant Signal Behav, 2014. 9(11): p. e977734 [PMID:25531128] Nemie-Feyissa D,Heidari B,Blaise M,Lillo C Analysis of interactions between heterologously produced bHLH and MYB proteins that regulate anthocyanin biosynthesis: quantitative interaction kinetics by Microscale Thermophoresis. Phytochemistry, 2015. 111: p. 21-6 [PMID:25659750] Kwak SH,Song SK,Lee MM,Schiefelbein J TORNADO1 regulates root epidermal patterning through the WEREWOLF pathway in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(12): p. e1103407 [PMID:26451798] Dai X, et al. A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3. Plant Cell Environ., 2016. 39(4): p. 897-907 [PMID:26667588] Friede A, et al. The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves. Front Plant Sci, 2017. 8: p. 1382 [PMID:28848584] Feng K, et al. An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica. Planta, 2018. 247(2): p. 301-315 [PMID:28965159] Wen J, et al. The C-terminal domains of Arabidopsis GL3/EGL3/TT8 interact with JAZ proteins and mediate dimeric interactions. Plant Signal Behav, 2018. 13(1): p. e1422460 [PMID:29293407]