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

Rsa1.0_00127.1_g00026.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

MYB

Protein Properties

Length: 250aa MW: 28897.2 Da PI: 10.4067

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00127.1_g00026.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	51.3	2.7e-16	19	64	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 rg W + Ed+ l ++v+q+G+++W+ Ia+++ gR++k+c++rw++ Rsa1.0_00127.1_g00026.1 19 RGHWRPIEDDHLRQLVEQYGPKNWNFIAQHLH-GRSGKSCRLRWYNQ 64 899***************************.**********96 PP
2	Myb_DNA-binding	55	1.9e-17	71	114	1	46
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 ++++T+eE+e+l++a++ G++ W++Iar ++ gRt++ +k++++ Rsa1.0_00127.1_g00026.1 71 KKPFTEEEEERLLKAHRIQGNR-WASIARLFP-GRTDNAVKNHFHV 114 689*****************.*****.********986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	16.574	14	65	IPR017930	Myb domain
SMART	SM00717	5.7E-14	18	67	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	1.05E-28	18	112	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	8.6E-26	20	72	IPR009057	Homeodomain-like
CDD	cd00167	1.08E-12	22	63	No hit	No description
Pfam	PF13921	8.9E-17	22	82	No hit	No description
PROSITE profile	PS51294	23.198	66	120	IPR017930	Myb domain
SMART	SM00717	1.5E-14	70	118	IPR001005	SANT/Myb domain
CDD	cd00167	6.70E-11	73	113	No hit	No description
Gene3D	G3DSA:1.10.10.60	4.2E-20	73	118	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:2000652	Biological Process	regulation of secondary cell wall biogenesis
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 250 aa Download sequence Send to blast
MDMSRGSNSF DNKKASCQRG HWRPIEDDHL RQLVEQYGPK NWNFIAQHLH GRSGKSCRLR 60 WYNQLDPNIT KKPFTEEEEE RLLKAHRIQG NRWASIARLF PGRTDNAVKN HFHVIMARRK 120 RESHSSTATP TFNQSWHNIL SPSSSLTRFN RSQFGLWRYQ KDKSRGFRPC TFVSGPRDDE 180 FGSSSISNVR KEVYSERRKL KELVDQHNNA LDTATPDHKK NSVEDGPSTG DDGEKKNVAF 240 IDFLGVGLVS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1a5j_A	2e-33	19	119	7	107	B-MYB
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Acts as a cell-specific local repressor of quiescent center (QC) self-renewal by cell divisions in the primary root. Counteracts brassinosteroid (BR)-mediated cell division in the QC cells (PubMed:24981610). Regulates maternally seed size, especially before the heart stage, promoting both endothelial cells expansion and cell number in the outer integument layer of the seed coat (PubMed:23911125). Modulates the expression of genes involved in cell wall metabolism such as cell division and expansion (PubMed:23911125, PubMed:24981610). Negative regulator of flowering via the repression of FT transcription (PubMed:25343985). {ECO:0000269\|PubMed:23911125, ECO:0000269\|PubMed:24981610, ECO:0000269\|PubMed:25343985}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00127.1_g00026.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Levels follow a circadian cycle with a progressive decrease during the day time (at protein level) (PubMed:25343985). Down-regulated by brassinosteroids (BRs) in a dose- and time-dependent manner. Repressed by BES1. Auto-activation of expression (PubMed:24981610). Targeted to 26S proteasomal degradation by the CULLIN3 (CUL3)-based E3 ligases CRL3(BPMs) (PubMed:25343985). {ECO:0000269\|PubMed:24981610, ECO:0000269\|PubMed:25343985}.

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	AC189637	0.0	AC189637.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrS004O21, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013591863.1	1e-163	PREDICTED: transcriptional activator Myb
Refseq	XP_013660105.1	1e-163	transcription factor MYB105
Swissprot	Q6R053	6e-56	MYB56_ARATH; Transcription factor MYB56
TrEMBL	A0A0D3A288	1e-161	A0A0D3A288_BRAOL; Uncharacterized protein
TrEMBL	A0A1J3INR5	1e-161	A0A1J3INR5_NOCCA; Transcription factor MYB44 (Fragment)
STRING	Bo1g008140.1	1e-162	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM10133	20	36

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G33450.1	1e-155	myb domain protein 69

Publications ? help Back to Top
Chen L,Bernhardt A,Lee J,Hellmann H Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases. Mol Plant, 2015. [PMID:25343985] Frigola D,Caño-Delgado AI,Ibañes M Methods for Modeling Brassinosteroid-Mediated Signaling in Plant Development. Methods Mol. Biol., 2017. 1564: p. 103-120 [PMID:28124249] Espinosa-Ruiz A, et al. TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana. Development, 2017. 144(9): p. 1619-1628 [PMID:28320734] Jeong CY, et al. AtMyb56 Regulates Anthocyanin Levels via the Modulation of AtGPT2 Expression in Response to Sucrose in Arabidopsis. Mol. Cells, 2018. 41(4): p. 351-361 [PMID:29487277]