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

GSBRNA2T00025350001

Common Name

GSBRNA2T00025350001

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: 578aa MW: 64138.6 Da PI: 6.2134

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00025350001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	40.5	4.9e-13	382	429	3	55
HHHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 3 rahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 ++h E++RR+++N++f Lr+++P+ + K +K++iL ++eY+++L+ GSBRNA2T00025350001 382 ANHAVSEKKRREKLNERFLILRSIIPSiN------KSDKVSILDDTIEYLQELE 429 58999********************77......99************995 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	5.3E-52	14	206	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	16.336	379	428	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.23E-17	381	444	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.0E-10	382	429	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.85E-13	383	433	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.3E-17	383	445	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.3E-14	385	434	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:0010091	Biological Process	trichome branching
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 578 aa Download sequence Send to blast
MVTGQNRTSV PENLKKQLAI SIRSIQWSYA IFWSVSASQP GVLEWGDGYY NGDIKTRKTI 60 QASEIKADQL GLRRSEQLRE LFESLSIAES SSTGTAAGSQ VSRRASAAAL SPEDLADTEW 120 YYLVCMSFVF KIGEGMPGRT FANGEPIWLC NAGTADSKVF SRSLLAKSAS VNTVICFPFL 180 GGVVEIGTTE HIAEDMNVIQ CVKKSFLEAP DSNATILQPI SSDYHIDNVL DPQHILEDEI 240 YAPMFGTRPF QATSPSRTTN GFDPEHDQLA EDHDSFMAEG INSQKNVKML SFDPRNDDVH 300 YQSVISTIFK TSHQLILGPQ FRNCDKRSSF TRWKKPSPSS CGTASIVAPS QGMLKKIIFE 360 VPRVHQKEKL MLDSPVAGDE TANHAVSEKK RREKLNERFL ILRSIIPSIN KSDKVSILDD 420 TIEYLQELER RVQELESCRE STDTETRGTI TVKRKKPYDA GERTSANCTN NEIGYVKRTH 480 VGEAEPAETG LTDIRIRSFG NEVVIELRCV WREGVLLEIM DVISNLNLDS HSVQSSTGDG 540 LLCLTVSCKH KGSKIATPGM IKEALKRLHG YVEDILA*

Sequence ? help Back to Top

Protein Sequence Length: 578 aa Download sequence Send to blast

MVTGQNRTSV PENLKKQLAI SIRSIQWSYA IFWSVSASQP GVLEWGDGYY NGDIKTRKTI  60
QASEIKADQL GLRRSEQLRE LFESLSIAES SSTGTAAGSQ VSRRASAAAL SPEDLADTEW  120
YYLVCMSFVF KIGEGMPGRT FANGEPIWLC NAGTADSKVF SRSLLAKSAS VNTVICFPFL  180
GGVVEIGTTE HIAEDMNVIQ CVKKSFLEAP DSNATILQPI SSDYHIDNVL DPQHILEDEI  240
YAPMFGTRPF QATSPSRTTN GFDPEHDQLA EDHDSFMAEG INSQKNVKML SFDPRNDDVH  300
YQSVISTIFK TSHQLILGPQ FRNCDKRSSF TRWKKPSPSS CGTASIVAPS QGMLKKIIFE  360
VPRVHQKEKL MLDSPVAGDE TANHAVSEKK RREKLNERFL ILRSIIPSIN KSDKVSILDD  420
TIEYLQELER RVQELESCRE STDTETRGTI TVKRKKPYDA GERTSANCTN NEIGYVKRTH  480
VGEAEPAETG LTDIRIRSFG NEVVIELRCV WREGVLLEIM DVISNLNLDS HSVQSSTGDG  540
LLCLTVSCKH KGSKIATPGM IKEALKRLHG YVEDILA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rqw_A	3e-17	12	206	7	192	Transcription factor MYC3
4rqw_B	3e-17	12	206	7	192	Transcription factor MYC3
4rs9_A	3e-17	12	206	7	192	Transcription factor MYC3
4yz6_A	3e-17	12	206	7	192	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	388	393	KKRREK

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: Mostly expressed in roots and flowers. Also present in stems and leaves, and, to a lower extent, in hypocotyls. 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:12679534, 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, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication. Regulates also trichome cell wall maturation. 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. Activates the transcription of GL2. {ECO:0000269\|PubMed:11063707, ECO:0000269\|PubMed:12917293, ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14561633, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15590742}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00025350001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By nitrogen deficiency and UV light. 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, ECO:0000269\|PubMed:17053893}.

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_013632341.1	0.0	PREDICTED: LOW QUALITY PROTEIN: transcription factor GLABRA 3
Swissprot	Q9FN69	0.0	GL3_ARATH; Transcription factor GLABRA 3
TrEMBL	A0A078J763	0.0	A0A078J763_BRANA; BnaCnng33960D protein
STRING	Bra025508.1-P	0.0	(Brassica rapa)

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
AT5G41315.1	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] Nemie-Feyissa D,Olafsdottir SM,Heidari B,Lillo C Nitrogen depletion and small R3-MYB transcription factors affecting anthocyanin accumulation in Arabidopsis leaves. Phytochemistry, 2014. 98: p. 34-40 [PMID:24388610] 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] 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] Wada T,Kunihiro A,Tominaga-Wada R Arabidopsis CAPRICE (MYB) and GLABRA3 (bHLH) control tomato (Solanum lycopersicum) anthocyanin biosynthesis. PLoS ONE, 2014. 9(9): p. e109093 [PMID:25268379] 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] Sun L, et al. GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis. New Phytol., 2015. 206(1): p. 220-30 [PMID:25640859] 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] Yu D, et al. RPN1a, a subunit of the 26S proteasome, controls trichome development in Arabidopsis. Plant Physiol. Biochem., 2015. 88: p. 82-8 [PMID:25676129] Huang M,Hu Y,Liu X,Li Y,Hou X Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development. Front Plant Sci, 2015. 6: p. 955 [PMID:26579186] 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] Pan Y,Bo K,Cheng Z,Weng Y The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1. BMC Plant Biol., 2015. 15: p. 302 [PMID:26714637] Alahakoon UI, et al. Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity. BMC Plant Biol., 2016. 16: p. 12 [PMID:26739276] Zheng K, et al. Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation. Sci Rep, 2016. 6: p. 19254 [PMID:26758286] Shangguan XX,Yang CQ,Zhang XF,Wang LJ Functional characterization of a basic helix-loop-helix (bHLH) transcription factor GhDEL65 from cotton (Gossypium hirsutum). Physiol Plant, 2016. 158(2): p. 200-12 [PMID:27080593] Petridis A,Döll S,Nichelmann L,Bilger W,Mock HP Arabidopsis thaliana G2-LIKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low-temperature regulators of flavonoid accumulation. New Phytol., 2016. 211(3): p. 912-25 [PMID:27125220] Gao C, et al. Genome-wide identification of GLABRA3 downstream genes for anthocyanin biosynthesis and trichome formation in Arabidopsis. Biochem. Biophys. Res. Commun., 2017. 485(2): p. 360-365 [PMID:28216162] 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] Gao C, et al. Brassica napusGLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana. Plant Biol (Stuttg), 2018. 20(1): p. 3-9 [PMID:28940939] 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] Kim SY,Hyoung S,So WM,Shin JS The novel transcription factor TRP interacts with ZFP5, a trichome initiation-related transcription factor, and negatively regulates trichome initiation through gibberellic acid signaling. Plant Mol. Biol., 2018. 96(3): p. 315-326 [PMID:29335898]