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

GSBRNA2T00016228001

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: 252aa MW: 28869.6 Da PI: 9.7161

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00016228001	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	55.8	1.1e-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++ GSBRNA2T00016228001 5 RGHWRPAEDEKLKELVQQFGPHNWNAIAQKLT-GRSGKSCRLRWFNQ 50 899**************************9.*********996 PP
2	Myb_DNA-binding	53.5	5.6e-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+ GSBRNA2T00016228001 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	24.136	1	55	IPR017930	Myb domain
SMART	SM00717	1.7E-14	4	53	IPR001005	SANT/Myb domain
Pfam	PF00249	7.8E-17	5	50	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	6.36E-30	5	98	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	3.9E-27	6	58	IPR009057	Homeodomain-like
CDD	cd00167	3.44E-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	4.0E-14	57	99	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	1.7E-20	59	104	IPR009057	Homeodomain-like
CDD	cd00167	6.65E-12	59	99	No hit	No description

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: 252 aa Download sequence Send to blast
MMCSRGHWRP AEDEKLKELV QQFGPHNWNA IAQKLTGRSG KSCRLRWFNQ LDPRINRTPF 60 TEEEEKRLLA SHRIHGNRWS VIARFFPGRT DNAVKNHWHV IMARRGRELS KLRPRGLGHD 120 GTTAATIGYD GCDKKRRLAT ASTISYPHQF SHISLCLSHF QLLKEFLTGK IGLFNNTTSI 180 NEGAINQTKR PIEFYDFLQV KTDSKKPEVI DNSRKYEEED GVSEHNHNHN ENCVPFIDFL 240 SVGNSASQSL C*

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	GSBRNA2T00016228001

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009117637.1	1e-178	PREDICTED: transcription factor MYB44-like
Refseq	XP_013660229.1	1e-178	transcription factor MYB52-like
Swissprot	Q6R0C4	1e-149	MYB52_ARATH; Transcription factor MYB52
TrEMBL	A0A078G9M9	0.0	A0A078G9M9_BRANA; BnaA09g44780D protein
STRING	Bra031008.1-P	1e-178	(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-151	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]