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_00166.1_g00016.1

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: 227aa MW: 26652.8 Da PI: 9.8471

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00166.1_g00016.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	90.9	6.6e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRr+g+lKKA+ELSvLCda+va ++fs++gklyey+s Rsa1.0_00166.1_g00016.1 9 KRIENLTSRQVTFSKRRKGLLKKAHELSVLCDAQVAAVVFSQKGKLYEYAS 59 79***********************************************86 PP
2	K-box	49.7	1.6e-17	83	173	9	96
K-box 9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk...ekelqeen 91 ++e++ + l++e++ + + ie Lqr R+l+G+dL+s+sl+eL+++ q+eksl+ +Rs+K l e++++l+ ++el +e Rsa1.0_00166.1_g00016.1 83 QKEQQVQDLKNEITIMVNSIELLQRHCRRLMGQDLDSCSLEELKEITIQIEKSLTIVRSRKATLNEEEVRKLKAEiagKRELLNER 168 68999*****************************************************************9997522245555555 PP K-box 92 kaLrk 96 ++L++ Rsa1.0_00166.1_g00016.1 169 TRLHQ 173 55655 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	8.1E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.413	1	61	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.3E-30	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.01E-30	3	71	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.83E-38	3	68	No hit	No description
Pfam	PF00319	2.2E-25	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.3E-30	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.3E-30	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	6.1E-17	84	174	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	11	88	184	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: 227 aa Download sequence Send to blast
MVRGKIEIKR IENLTSRQVT FSKRRKGLLK KAHELSVLCD AQVAAVVFSQ KGKLYEYASS 60 DMKKMMERCE IHRREYFHAE RFQKEQQVQD LKNEITIMVN SIELLQRHCR RLMGQDLDSC 120 SLEELKEITI QIEKSLTIVR SRKATLNEEE VRKLKAEIAG KRELLNERTR LHQMETKLLS 180 FQFEEKPLWT QSRNLESEKN ASSSASENMH ISNVETDLFI GLPRSRV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	6e-19	1	66	1	66	MEF2C
5f28_B	6e-19	1	66	1	66	MEF2C
5f28_C	6e-19	1	66	1	66	MEF2C
5f28_D	6e-19	1	66	1	66	MEF2C
6byy_A	5e-19	1	66	1	66	MEF2 CHIMERA
6byy_B	5e-19	1	66	1	66	MEF2 CHIMERA
6byy_C	5e-19	1	66	1	66	MEF2 CHIMERA
6byy_D	5e-19	1	66	1	66	MEF2 CHIMERA
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Functional Description ? help Back to Top
Source	Description
UniProt	MADS-box transcription factor that acts with AGL42 and AGL71 in the control of flowering time. Promotes flowering at the shoot apical and axillary meristems. Seems to act through a gibberellin-dependent pathway. Interacts genetically with SOC1 and its expression is directly regulated by SOC1. {ECO:0000269\|PubMed:21609362}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00166.1_g00016.1

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	AC232542	8e-80	AC232542.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH005L20, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018437428.1	1e-156	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437429.1	1e-156	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437430.1	1e-156	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437431.1	1e-156	PREDICTED: MADS-box protein AGL71-like
Swissprot	Q9FLH5	7e-74	AGL72_ARATH; MADS-box protein AGL72
TrEMBL	A0A078HZW3	1e-140	A0A078HZW3_BRANA; BnaAnng06990D protein
TrEMBL	A0A398AGB5	1e-140	A0A398AGB5_BRACM; Uncharacterized protein
TrEMBL	A0A3P6B971	1e-140	A0A3P6B971_BRACM; Uncharacterized protein
STRING	Bo2g161560.1	1e-136	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8805	12	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G51860.2	9e-75	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]