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

Rsa1.0_01249.1_g00010.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 269aa MW: 30464.1 Da PI: 7.0492

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01249.1_g00010.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	43.1	1e-13	11	56	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 + Rsa1.0_01249.1_g00010.1 11 KGPWKAEEDEVLINHVKRYGPRDWSSIRSKGLLQRTGKSCRLRWVN 56 79***********************8887799********87 PP
2	Myb_DNA-binding	45.9	1.3e-14	67	107	3	45
SS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHH CS Myb_DNA-binding 3 rWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwq 45 ++++eE++ +d+ q+G++ W++Ia +++ gRt++++k++w Rsa1.0_01249.1_g00010.1 67 KFSAEEEKTVIDLQSQFGNK-WARIATYLP-GRTDNDVKNFWS 107 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	5	59	IPR009057	Homeodomain-like
PROSITE profile	PS51294	21.64	6	62	IPR017930	Myb domain
SuperFamily	SSF46689	5.24E-28	8	106	IPR009057	Homeodomain-like
SMART	SM00717	7.1E-11	10	60	IPR001005	SANT/Myb domain
CDD	cd00167	4.92E-11	13	58	No hit	No description
Pfam	PF13921	6.4E-12	14	64	No hit	No description
Gene3D	G3DSA:1.10.10.60	6.7E-19	60	112	IPR009057	Homeodomain-like
PROSITE profile	PS51294	18.216	63	114	IPR017930	Myb domain
SMART	SM00717	8.5E-13	64	112	IPR001005	SANT/Myb domain
Pfam	PF00249	9.7E-13	67	107	IPR001005	SANT/Myb domain
CDD	cd00167	3.54E-10	67	106	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0048235	Biological Process	pollen sperm cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 269 aa Download sequence Send to blast
MEAAKKEDIK KGPWKAEEDE VLINHVKRYG PRDWSSIRSK GLLQRTGKSC RLRWVNKLRP 60 NLKNGCKFSA EEEKTVIDLQ SQFGNKWARI ATYLPGRTDN DVKNFWSSRL KRLARILHNS 120 SDASSSSCLN PKPSKGKNVK PIQSQSIGFV EEETRASSSS TSKILPYSSS SADQVVDEAL 180 IRSPELGIRL ENHQPFTFGT DLDDPFFYDI LGPADSSEPL FGIPQPFFEP SPAPRRFRHV 240 SKEDEESDVF LHDFPADMFD QVDDQTTSP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1h8a_C	9e-28	8	112	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01249.1_g00010.1

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-135	DUO1_ARATH; Transcription factor DUO1
TrEMBL	A0A3P6GD57	0.0	A0A3P6GD57_BRAOL; Uncharacterized protein
STRING	Bra007536.1-P	0.0	(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-132	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]