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

GSBRNA2T00059552001

Common Name

GSBRNA2T00016228001

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

MYB

Protein Properties

Length: 158aa MW: 18207.8 Da PI: 11.3154

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00059552001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	56.9	4.7e-18	4	49	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++ GSBRNA2T00059552001 4 RGHWRPAEDEKLKELVQQFGPHNWNAIAQKLT-GRSGKSCRLRWFNQ 49 899**************************9.*********996 PP
2	Myb_DNA-binding	54.6	2.5e-17	56	99	1	46
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 r ++T+eE+++l+ ++ +G++ W+ Iar ++ gRt++ +k++w+ GSBRNA2T00059552001 56 RTPFTEEEEKRLLASHRIHGNR-WSVIARFFP-GRTDNAVKNHWHV 99 679*****************.*****.*********96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	24.158	1	54	IPR017930	Myb domain
SMART	SM00717	1.7E-14	3	52	IPR001005	SANT/Myb domain
Pfam	PF00249	3.4E-17	4	49	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	2.13E-30	4	97	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	1.5E-27	5	57	IPR009057	Homeodomain-like
CDD	cd00167	4.32E-13	7	48	No hit	No description
PROSITE profile	PS51294	18.517	55	105	IPR017930	Myb domain
SMART	SM00717	2.8E-15	55	103	IPR001005	SANT/Myb domain
Pfam	PF00249	1.8E-14	56	98	IPR001005	SANT/Myb domain
CDD	cd00167	7.80E-12	58	98	No hit	No description
Gene3D	G3DSA:1.10.10.60	6.9E-21	58	103	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: 158 aa Download sequence Send to blast
MCSRGHWRPA EDEKLKELVQ QFGPHNWNAI AQKLTGRSGK SCRLRWFNQL DPRINRTPFT 60 EEEEKRLLAS HRIHGNRWSV IARFFPGRTD NAVKNHWHVI MARRGRELSK LRPRGLGHDG 120 TTAATIGYDG CDKKRRLATA STISYPHQFS HISLCLR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1mse_C	2e-33	1	104	1	104	C-Myb DNA-Binding Domain
1msf_C	2e-33	1	104	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	GSBRNA2T00059552001

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	AY086672	1e-144	AY086672.1 Arabidopsis thaliana clone 267121 mRNA, complete sequence.
GenBank	AY519554	1e-144	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_009117637.1	1e-108	PREDICTED: transcription factor MYB44-like
Refseq	XP_013660229.1	1e-108	transcription factor MYB52-like
Swissprot	Q6R0C4	3e-98	MYB52_ARATH; Transcription factor MYB52
TrEMBL	A0A078G9M9	1e-113	A0A078G9M9_BRANA; BnaA09g44780D protein
TrEMBL	A0A078HDV6	1e-114	A0A078HDV6_BRANA; BnaA05g29580D protein
STRING	Bra031008.1-P	1e-108	(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-100	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] 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] Shi D, et al. MYB52 Negatively Regulates Pectin Demethylesterification in Seed Coat Mucilage. Plant Physiol., 2018. 176(4): p. 2737-2749 [PMID:29440562]