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_009110374.1

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

MYB

Protein Properties

Length: 242aa MW: 28159.8 Da PI: 9.2883

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009110374.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	55.3	1.5e-17	5	50	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 rg W + Ede+l ++v+q+G+++W++Ia+++ gR++k+c++rw++ XP_009110374.1 5 RGHWRPAEDEKLRELVQQFGPHNWNAIAQKLT-GRSGKSCRLRWFNQ 50 899**************************9.*********996 PP
2	Myb_DNA-binding	53.6	5.2e-17	57	100	1	46
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 r ++T+eE+++l+ ++ +G++ W+ Iar ++ gRt++ +k++w+ XP_009110374.1 57 RTPFTEEEEKRLLASHRIHGNR-WSVIARFFP-GRTDNAVKNHWHV 100 679*****************.*****.*********96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	24.334	1	55	IPR017930	Myb domain
SMART	SM00717	2.3E-14	4	53	IPR001005	SANT/Myb domain
Pfam	PF00249	7.9E-17	5	50	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	5.24E-30	5	98	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	3.0E-27	6	58	IPR009057	Homeodomain-like
CDD	cd00167	2.85E-13	8	49	No hit	No description
SMART	SM00717	2.8E-15	56	104	IPR001005	SANT/Myb domain
PROSITE profile	PS51294	18.517	56	106	IPR017930	Myb domain
Pfam	PF00249	3.8E-14	57	99	IPR001005	SANT/Myb domain
CDD	cd00167	4.50E-12	59	99	No hit	No description
Gene3D	G3DSA:1.10.10.60	1.6E-20	59	104	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 242 aa Download sequence Send to blast
MMCSRGHWRP AEDEKLRELV QQFGPHNWNA IAQKLTGRSG KSCRLRWFNQ LDPRINRTPF 60 TEEEEKRLLA SHRIHGNRWS VIARFFPGRT DNAVKNHWHV IMARRGRERS KMRPRSLGHD 120 GTEAGPGMMG YKDCDKKRRL ATTIDINYPY SFSHINHFQI LKEFLTGKIG FCNSTTPMNE 180 GALDQTKRPM EFYNFLQVKT DSKPEVIHNS RKEEDEDEED VDNCVPFFDF LSVGNSASKG 240 LC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1mse_C	2e-32	2	105	1	104	C-Myb DNA-Binding Domain
1msf_C	2e-32	2	105	1	104	C-Myb DNA-Binding Domain
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in stamen (PubMed:19325888). Present in roots and siliques, and, at low levels, in leaves and flowers (PubMed:21399993). Expressed in stems, especially in fibers and, at lower levels, in xylems (PubMed:18952777, PubMed:21399993). {ECO:0000269\|PubMed:18952777, ECO:0000269\|PubMed:19325888, ECO:0000269\|PubMed:21399993}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that confers sensitivity to abscisic acid (ABA) and salt, but tolerance to drought (PubMed:21399993). Regulates secondary cell wall (SCW) biosynthesis, especially in interfascicular and xylary fibers (PubMed:18952777, PubMed:23781226). {ECO:0000269\|PubMed:18952777, ECO:0000269\|PubMed:21399993, ECO:0000269\|PubMed:23781226}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009110374.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By abscisic acid (PubMed:16463103, PubMed:21399993). Accumulates in response to salt (PubMed:21399993). Triggered by MYB46 and MYB83 in the regulation of secondary cell wall biosynthesis (PubMed:19674407, PubMed:22197883). {ECO:0000269\|PubMed:16463103, ECO:0000269\|PubMed:19674407, ECO:0000269\|PubMed:21399993, ECO:0000269\|PubMed:22197883}.

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	AY519554	0.0	AY519554.1 Arabidopsis thaliana MYB transcription factor (At1g17950) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009110374.1	0.0	PREDICTED: transcriptional activator Myb-like
Swissprot	Q6R0C4	1e-155	MYB52_ARATH; Transcription factor MYB52
TrEMBL	M4DJ97	0.0	M4DJ97_BRARP; Uncharacterized protein
STRING	Bra016575.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2818	27	69

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G17950.1	1e-154	myb domain protein 52

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] Cassan-Wang H, et al. Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis. Front Plant Sci, 2013. 4: p. 189 [PMID:23781226] Shi D, et al. MYB52 Negatively Regulates Pectin Demethylesterification in Seed Coat Mucilage. Plant Physiol., 2018. 176(4): p. 2737-2749 [PMID:29440562]