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

RrC4032_p4

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: 61aa MW: 6954.17 Da PI: 10.6628

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4032_p4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	96.5	1.2e-30	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRr+g+lKKA+ELSvLCda+va i+fs++gklyey+s RrC4032_p4 9 KRIENLTSRQVTFSKRRKGLLKKAHELSVLCDAQVAAIVFSQKGKLYEYAS 59 79***********************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.0E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.469	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	9.66E-36	3	60	No hit	No description
SuperFamily	SSF55455	2.09E-29	3	60	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.0E-31	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	8.9E-27	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.0E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.0E-31	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: 61 aa Download sequence Send to blast
MVRGKIEIKR IENLTSRQVT FSKRRKGLLK KAHELSVLCD AQVAAIVFSQ KGKLYEYASS 60 E

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	6e-19	1	61	1	61	MEF2C
5f28_B	6e-19	1	61	1	61	MEF2C
5f28_C	6e-19	1	61	1	61	MEF2C
5f28_D	6e-19	1	61	1	61	MEF2C
Search in ModeBase

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}.

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	3e-85	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	7e-35	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437429.1	7e-35	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437430.1	7e-35	PREDICTED: MADS-box protein AGL71-like
Refseq	XP_018437431.1	7e-35	PREDICTED: MADS-box protein AGL71-like
Swissprot	Q9FLH5	6e-32	AGL72_ARATH; MADS-box protein AGL72
TrEMBL	A0A0D3DDL6	5e-34	A0A0D3DDL6_BRAOL; Uncharacterized protein
TrEMBL	A0A3N6RXN1	5e-34	A0A3N6RXN1_BRACR; Uncharacterized protein
STRING	Bo7g098670.1	9e-35	(Brassica oleracea)

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
AT5G51860.2	2e-34	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]