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

GSBRNA2T00038925001

Common Name

GSBRNA2T00038925001, LOC106399792

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: 336aa MW: 37463.7 Da PI: 6.1754

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00038925001	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	48	2.9e-15	32	79	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g W+++Ede+l+++ G g+W+ Iar g+ R++k+c++rw +yl GSBRNA2T00038925001 32 KGLWSPDEDEKLIRYMLTNGQGCWSDIARNAGLLRCGKSCRLRWINYL 79 678***************************99**********97 PP
2	Myb_DNA-binding	48.2	2.6e-15	85	129	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 rg+++++E++l+ +++ lG++ W+ Ia +++ gRt++++k++w++ GSBRNA2T00038925001 85 RGSFSPQEEDLIFHLHSILGNR-WSQIATRLP-GRTDNEIKNFWNST 129 899*****************.*****.*********986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	2.7E-22	26	82	IPR009057	Homeodomain-like
PROSITE profile	PS51294	17.309	27	79	IPR017930	Myb domain
SuperFamily	SSF46689	1.13E-27	29	126	IPR009057	Homeodomain-like
SMART	SM00717	1.7E-12	31	81	IPR001005	SANT/Myb domain
Pfam	PF00249	6.4E-14	32	79	IPR001005	SANT/Myb domain
CDD	cd00167	3.31E-10	35	79	No hit	No description
PROSITE profile	PS51294	25.467	80	134	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	2.2E-25	83	135	IPR009057	Homeodomain-like
SMART	SM00717	1.4E-15	84	132	IPR001005	SANT/Myb domain
Pfam	PF00249	4.2E-14	85	129	IPR001005	SANT/Myb domain
CDD	cd00167	7.97E-11	87	130	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: 336 aa Download sequence Send to blast
MMMRNQDITT IRDKNKASNA CGGNNNKPKL RKGLWSPDED EKLIRYMLTN GQGCWSDIAR 60 NAGLLRCGKS CRLRWINYLR PDLKRGSFSP QEEDLIFHLH SILGNRWSQI ATRLPGRTDN 120 EIKNFWNSTL KKKLKNNNTS SGSSPNNSNS NSLEPIDQHV DMGGNSNPMM NSHHHQDDMM 180 IVGNTMHMES SSFHAPVVSG VGLNQLDPLI SVTDHNRYQQ MANTGNNNVN GLGDYGSAVL 240 DPISNRASVE NEWFLPPSEN TNGIACATSN NLNLEALDPC FGSKNMCHSE SFKVGNIMGM 300 ENSSWEIENP KIGDWDLDSL IDNNSSFPFL DFQVE*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1h8a_C	2e-29	14	134	6	128	MYB TRANSFORMING PROTEIN
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed specifically in fiber and vessel cells that are undergoing secondary wall thickening in floral stems. Expressed in vessels but not in xylary fibers in the developing secondary xylem of roots. {ECO:0000269\|PubMed:19808805}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1 and its close homologs, including NAC043/NST1, NAC066/NST2, NAC101/VND6 and NAC030/VND7. Is required for functional expression of a number of secondary wall-associated transcription factors and secondary wall biosynthetic genes involved in cellulose, xylan and lignin synthesis. Functions redundantly with MYB46 in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels (PubMed:19808805). Transcription activator that binds to the DNA consensus sequence 5'-ACC[AT]A[AC][TC]-3', designated as the secondary wall MYB-responsive element (SMRE). Regulates directly numerous transcription factors and a number of genes involved in secondary wall biosynthesis that contain SMRE elements in their promoters (PubMed:22197883). {ECO:0000269\|PubMed:19808805, ECO:0000269\|PubMed:22197883}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00038925001

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	AC189368	0.0	AC189368.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB047A09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013695698.1	0.0	transcription factor MYB83
Swissprot	Q9C6U1	0.0	MYB83_ARATH; Transcription factor MYB83
TrEMBL	A0A078GS52	0.0	A0A078GS52_BRANA; BnaC05g44010D protein
STRING	Bo5g139830.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7077	26	42

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G08500.1	1e-179	myb domain protein 83

Link Out ? help Back to Top
Entrez Gene	106399792

Publications ? help Back to Top
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] Vargas L, et al. Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants. Biotechnol Biofuels, 2016. 9: p. 139 [PMID:27390589] Piya S,Kihm C,Rice JH,Baum TJ,Hewezi T Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism. Plant Physiol., 2017. 174(3): p. 1897-1912 [PMID:28512179]