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

RrC7993_p1

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

M-type_MADS

Protein Properties

Length: 62aa MW: 6973.21 Da PI: 11.6253

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC7993_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	78.5	4.7e-25	9	55	1	47
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgkly 47 krienks rqvtf+kRrng++KKA LS+LC+ va++i+sstgkly RrC7993_p1 9 KRIENKSSRQVTFCKRRNGLMKKARQLSILCESSVAILIVSSTGKLY 55 79********************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF55455	3.14E-25	1	58	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	28.399	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.0E-32	1	60	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.4E-25	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	4.3E-24	10	56	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.4E-25	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.4E-25	38	59	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 62 aa Download sequence Send to blast
MGRRKVEIKR IENKSSRQVT FCKRRNGLMK KARQLSILCE SSVAILIVSS TGKLYSSSAG 60 DR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	1e-17	1	61	1	61	MEF2C
5f28_B	1e-17	1	61	1	61	MEF2C
5f28_C	1e-17	1	61	1	61	MEF2C
5f28_D	1e-17	1	61	1	61	MEF2C
Search in ModeBase

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}.

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC166741	3e-82	AC166741.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH080C09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018439876.1	3e-35	PREDICTED: protein MADS AFFECTING FLOWERING 5-like
Swissprot	Q683D7	3e-32	MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBL	A0A078H0K5	2e-33	A0A078H0K5_BRANA; BnaA02g34550D protein
TrEMBL	M4ESV4	2e-33	M4ESV4_BRARP; Uncharacterized protein
STRING	Bra031884.1-P	3e-34	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM78	28	413

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G65070.3	2e-35	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]