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_00073.1_g00005.1

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

MIKC_MADS

Protein Properties

Length: 211aa MW: 24143.2 Da PI: 10.1544

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00073.1_g00005.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	71.8	6e-23	9	55	1	47
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgkly 47 kr enks rqvtf+kRrng++KKA LS+LC+ va++i+sstgkly Rsa1.0_00073.1_g00005.1 9 KRMENKSSRQVTFCKRRNGLMKKARQLSILCESSVAILIVSSTGKLY 55 799*******************************************9 PP
2	K-box	22.1	6.2e-09	112	151	46	85
K-box 46 LslkeLqqLeqqLekslkkiRskKnellleqieelqkkek 85 +s++ L +Le+q +++l+ R++K el++e +++lq+k + Rsa1.0_00073.1_g00005.1 112 ISVEFLISLEEQFKSALSVTRARKAELMMELVKTLQEKVN 151 678889*******************************975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	28.02	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	8.3E-32	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	9.94E-26	1	73	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.7E-23	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	6.5E-22	10	56	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.7E-23	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.7E-23	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	9.215	70	182	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 211 aa Download sequence Send to blast
MGRRKVEIKR MENKSSRQVT FCKRRNGLMK KARQLSILCE SSVAILIVSS TGKLYSSSAG 60 DSMANILKRY EIQHADELKT VDLAEKNRDY LSHKELLEIV QCKLEEAKSG NISVEFLISL 120 EEQFKSALSV TRARKAELMM ELVKTLQEKV NARVLFAVLA TEKVLREEKK VLATQLTKME 180 KNRFLEAEDE RAMSLAKDFR NNTPETLSLL K

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	5e-16	1	80	1	80	MEF2C
5f28_B	5e-16	1	80	1	80	MEF2C
5f28_C	5e-16	1	80	1	80	MEF2C
5f28_D	5e-16	1	80	1	80	MEF2C
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in the negative regulation of flowering time in short days, probably through the photoperiodic and vernalization pathways. Prevents premature flowering, particularly in the cv. Landsberg erecta background. In non-inductive photoperiods (e.g. short days), required for flowering through VIL2-mediated maintenance of the epigenetically repressed state of MAF5 via H3K9me2 and plant homeodomain / polycomb repressive complex 2 (PHD-PRC2)-dependent H3K27me3. {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:18798874, ECO:0000269\|PubMed:18852898, ECO:0000269\|PubMed:20837520, ECO:0000269\|PubMed:21150261, ECO:0000269\|PubMed:21175890, ECO:0000269\|PubMed:21398257, ECO:0000269\|PubMed:22378382}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00073.1_g00005.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by vernalization. Repressed by VIL2, AGL6, CLF, EMF2 and FIE via epigenetic chromatin H3K27me3 and H3K9me2 regulation during the vegetative development. {ECO:0000269\|PubMed:12724541}.

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_018439876.1	1e-137	PREDICTED: protein MADS AFFECTING FLOWERING 5-like
Swissprot	Q683D7	1e-81	MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBL	A0A078H0K5	1e-117	A0A078H0K5_BRANA; BnaA02g34550D protein
STRING	Bra031884.1-P	1e-117	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM986	19	87

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G65070.1	1e-94	MIKC_MADS family protein

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] Conte MG,Gaillard S,Droc G,Perin C Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics, 2008. 9: p. 183 [PMID:18426584] Xu Y,Gan ES,Ito T The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5. Plant Signal Behav, 2014. [PMID:23733063] Liu B, et al. Interplay of the histone methyltransferases SDG8 and SDG26 in the regulation of transcription and plant flowering and development. Biochim. Biophys. Acta, 2016. 1859(4): p. 581-90 [PMID:26854085] Gong X,Shen L,Peng YZ,Gan Y,Yu H DNA Topoisomerase Iα Affects the Floral Transition. Plant Physiol., 2017. 173(1): p. 642-654 [PMID:27837087] Cui Z, et al. SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis. BMC Biol., 2017. 15(1): p. 80 [PMID:28893254]