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

Carubv10018791m

Common Name

CARUB_v10018791mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella

Family

MYB

Protein Properties

Length: 229aa MW: 26507.6 Da PI: 6.1676

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10018791m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	52.8	9e-17	16	63	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g WT eEd +l d+v +G+g+W++I r+ g++R++k+c++rw +yl Carubv10018791m 16 KGLWTVEEDNILMDYVLTHGTGQWNRIVRKTGLKRCGKSCRLRWMNYL 63 678*******************************************97 PP
2	Myb_DNA-binding	59.8	6e-19	69	114	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g +T++E++l+++++k+lG++ W++Ia++++ gRt++q+k++w+++l Carubv10018791m 69 KGTFTEQEEDLIIRLHKLLGNR-WSLIAKRVP-GRTDNQVKNYWNTHL 114 799*****************.*****.**********996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	17.918	11	63	IPR017930	Myb domain
SuperFamily	SSF46689	1.24E-30	14	110	IPR009057	Homeodomain-like
SMART	SM00717	5.3E-13	15	65	IPR001005	SANT/Myb domain
Pfam	PF00249	8.0E-15	16	63	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	4.3E-23	17	70	IPR009057	Homeodomain-like
CDD	cd00167	2.35E-10	19	63	No hit	No description
PROSITE profile	PS51294	28.108	64	118	IPR017930	Myb domain
SMART	SM00717	1.1E-18	68	116	IPR001005	SANT/Myb domain
Pfam	PF00249	3.7E-18	69	114	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	1.9E-27	71	118	IPR009057	Homeodomain-like
CDD	cd00167	3.42E-14	71	114	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0001708	Biological Process	cell fate specification
GO:0032880	Biological Process	regulation of protein localization
GO:0048629	Biological Process	trichome patterning
GO:2000039	Biological Process	regulation of trichome morphogenesis
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 229 aa Download sequence Send to blast
MRIRRREERE NQEFKKGLWT VEEDNILMDY VLTHGTGQWN RIVRKTGLKR CGKSCRLRWM 60 NYLSPNVNKG TFTEQEEDLI IRLHKLLGNR WSLIAKRVPG RTDNQVKNYW NTHLSKKLVG 120 DYPSAVKTTG DDEDSQPSLF ITATTTSSLH HQQENIYENL AKSFDNVVSA SYEDKPKPEP 180 DQTDVLVATT NDPSHYYGNN TLWDHEDEFE LSSLVMMNFA SGDIEYCL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1a5j_A	7e-29	16	118	7	108	B-MYB
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator, when associated with BHLH2/EGL3/MYC146 or BHLH12/MYC1. Involved in epidermal cell fate specification in leaves. Together with TTG1 and GL3, promotes trichome formation and endoreplication. Regulates the production of a signal that induces hair (trichome) precursor cells on leaf primordia to differentiate. Binds to the WER-binding sites (WBS) promoter regions and activates the transcription of target genes (By similarity). {ECO:0000250, ECO:0000269\|PubMed:11063707, ECO:0000269\|PubMed:12356720, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15728674, ECO:0000269\|PubMed:9625690}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10018791m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by gibberellins (PubMed:9625690). May be regulated by GEBP and GEBP-like proteins (PubMed:12535344). {ECO:0000269\|PubMed:12535344, ECO:0000269\|PubMed:9625690}.

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	AY519590	0.0	AY519590.1 Arabidopsis thaliana MYB transcription factor (At3g27920) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006292555.1	1e-172	trichome differentiation protein GL1
Swissprot	P27900	1e-154	GL1_ARATH; Trichome differentiation protein GL1
TrEMBL	R0HNH3	1e-171	R0HNH3_9BRAS; Uncharacterized protein
STRING	Cagra.4961s0006.1.p	1e-172	(Capsella grandiflora)
STRING	XP_006292555.1	1e-172	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4	28	2646

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G27920.1	1e-150	myb domain protein 0

Link Out ? help Back to Top
Phytozome	Carubv10018791m
Entrez Gene	17886658

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] 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] 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] 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] 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] Li Y, et al. Two IIIf Clade-bHLHs from Freesia hybrida Play Divergent Roles in Flavonoid Biosynthesis and Trichome Formation when Ectopically Expressed in Arabidopsis. Sci Rep, 2016. 6: p. 30514 [PMID:27465838] Hegebarth D,Buschhaus C,Wu M,Bird D,Jetter R The composition of surface wax on trichomes of Arabidopsis thaliana differs from wax on other epidermal cells. Plant J., 2016. 88(5): p. 762-774 [PMID:27496682] Busta L,Hegebarth D,Kroc E,Jetter R Changes in cuticular wax coverage and composition on developing Arabidopsis leaves are influenced by wax biosynthesis gene expression levels and trichome density. Planta, 2017. 245(2): p. 297-311 [PMID:27730411] Maxwell DJ,Partridge JC,Roberts NW,Boonham N,Foster GD The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS ONE, 2017. 12(3): p. e0174014 [PMID:28346494] García-Cano E,Hak H,Magori S,Lazarowitz SG,Citovsky V The Agrobacterium F-Box Protein Effector VirF Destabilizes the Arabidopsis GLABROUS1 Enhancer/Binding Protein-Like Transcription Factor VFP4, a Transcriptional Activator of Defense Response Genes. Mol. Plant Microbe Interact., 2018. 31(5): p. 576-586 [PMID:29264953] 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]