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

RrC1418_p3

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 271aa MW: 30874.7 Da PI: 7.5043

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1418_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	43	1e-13	14	59	1	46
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 +g+W +eEde l++ vk++G+++W++I ++ + Rt+k+c++rw + RrC1418_p3 14 KGPWKAEEDEVLINHVKRYGPRDWSSIRSKGLLQRTGKSCRLRWVN 59 79***********************8887799********87 PP
2	Myb_DNA-binding	47	6e-15	70	110	3	45
SS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHH CS Myb_DNA-binding 3 rWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwq 45 +++teE++ +d+ q+G++ W++Ia +++ gRt++++k++w RrC1418_p3 70 KFSTEEEKTVIDLQSQFGNK-WARIATYLP-GRTDNDVKNFWS 110 79****************.*****.*********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	1.5E-21	8	62	IPR009057	Homeodomain-like
PROSITE profile	PS51294	21.64	9	65	IPR017930	Myb domain
SuperFamily	SSF46689	6.36E-28	11	109	IPR009057	Homeodomain-like
SMART	SM00717	7.1E-11	13	63	IPR001005	SANT/Myb domain
CDD	cd00167	8.23E-11	16	61	No hit	No description
Pfam	PF13921	2.2E-13	17	78	No hit	No description
Gene3D	G3DSA:1.10.10.60	1.2E-18	63	115	IPR009057	Homeodomain-like
PROSITE profile	PS51294	17.924	66	117	IPR017930	Myb domain
SMART	SM00717	1.8E-12	67	115	IPR001005	SANT/Myb domain
CDD	cd00167	1.27E-9	70	109	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: 271 aa Download sequence Send to blast
MKKMEAAKKE DIKKGPWKAE EDEVLINHVK RYGPRDWSSI RSKGLLQRTG KSCRLRWVNK 60 LRPNLKNGCK FSTEEEKTVI DLQSQFGNKW ARIATYLPGR TDNDVKNFWS SRLKRLARIL 120 HNSSDASSSS CLNPKPSKGK NVKPIQSQSF GFVEEETRAS SSSCTKILPY SSSDQVVDEA 180 LIRSPELGIK LENHQPFTFG TDLDDPFFYD ILGPADSSEP LFGIPQPFFE PSPAPRRFRH 240 VSKEDDEESD VFLHDFPAEM FDQVDDQTTS P

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1h8a_C	1e-27	11	115	24	126	MYB TRANSFORMING PROTEIN
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that acts as a positive regulator of male germline development by promoting both gametic cell specification and cell cycle progression (PubMed:15694308, PubMed:15618418, PubMed:19300502, PubMed:21285328). Binds to canonical MYB sites 5'-AACCGTC-3', 5'-AAACCGC-3' and 5'-AACCGT-3' in promoters to trigger the expression of male germline-specific or enriched genes (e.g. MGH3, GEX2 and GCS1), including those required for fertilization (PubMed:21285328, PubMed:19300502). Required for sperm cell specification leading to pollen maturation by activating a germline-specific regulon (PubMed:21285328, PubMed:15694308, PubMed:15618418, PubMed:19300502). Involved in pollen mitosis entry at G2-M transition via the regulation of CYCB1-1, DAZ1 and DAZ2 expression (PubMed:15618418, PubMed:19300502, PubMed:24876252). {ECO:0000269\|PubMed:15618418, ECO:0000269\|PubMed:15694308, ECO:0000269\|PubMed:19300502, ECO:0000269\|PubMed:21285328, ECO:0000269\|PubMed:24876252}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the microRNA 159 (miR159); the production of miR159 is stimulated by the anaphase promoting complex/cyclosome (APC/C) (PubMed:21441434). Activated by ARID1 in male germline cells via specific histone acetylation regulation (e.g. H3K9Ac) (PubMed:25057814). {ECO:0000269\|PubMed:21441434, ECO:0000269\|PubMed:25057814}.

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	AC189319	0.0	AC189319.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB036H01, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018493179.1	0.0	PREDICTED: transcription factor MYB57
Swissprot	A0A178VEK7	1e-137	DUO1_ARATH; Transcription factor DUO1
TrEMBL	A0A078HUY5	1e-180	A0A078HUY5_BRANA; BnaA09g38510D protein
STRING	Bra007536.1-P	1e-178	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6551	28	42

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G60460.1	1e-137	MYB family protein

Publications ? help Back to Top
Zheng B,He H,Zheng Y,Wu W,McCormick S An ARID domain-containing protein within nuclear bodies is required for sperm cell formation in Arabidopsis thaliana. PLoS Genet., 2014. 10(7): p. e1004421 [PMID:25057814] Peters B, et al. A Conserved cis-Regulatory Module Determines Germline Fate through Activation of the Transcription Factor DUO1 Promoter. Plant Physiol., 2017. 173(1): p. 280-293 [PMID:27624837] Zheng Z, et al. Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy. Plant Physiol., 2017. 174(3): p. 1764-1778 [PMID:28515145]