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

RrC22842_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: 60aa MW: 6830.02 Da PI: 10.2891

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC22842_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	98.4	2.9e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs+t klye+ss RrC22842_p1 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPTSKLYEFSS 59 79***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	31.02	1	60	IPR002100	Transcription factor, MADS-box
SMART	SM00432	4.4E-39	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.44E-29	3	59	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	5.0E-31	3	23	IPR002100	Transcription factor, MADS-box
CDD	cd00265	4.45E-37	3	59	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	6.6E-28	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	5.0E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	5.0E-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: 60 aa Download sequence Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP TSKLYEFSSC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	1e-18	1	59	1	59	MEF2C
5f28_B	1e-18	1	59	1	59	MEF2C
5f28_C	1e-18	1	59	1	59	MEF2C
5f28_D	1e-18	1	59	1	59	MEF2C
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269\|PubMed:16778081}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269\|PubMed:16778081}.

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	AK230464	6e-59	AK230464.1 Arabidopsis thaliana mRNA for MADS-box protein AGL14, complete cds, clone: RAFL26-03-G06.
GenBank	AL078606	6e-59	AL078606.1 Arabidopsis thaliana DNA chromosome 4, BAC clone T26M18 (ESSA project).
GenBank	AL161532	6e-59	AL161532.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 32.
GenBank	AL161533	6e-59	AL161533.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 33.
GenBank	CP002687	6e-59	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018448945.1	8e-36	PREDICTED: agamous-like MADS-box protein AGL19 isoform X1
Refseq	XP_018448946.1	8e-36	PREDICTED: agamous-like MADS-box protein AGL19 isoform X1
Swissprot	O82743	2e-34	AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBL	A0A078HWX3	6e-34	A0A078HWX3_BRANA; BnaA01g12710D protein
STRING	Bra020826.1-P	2e-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
AT4G22950.1	8e-37	AGAMOUS-like 19

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] Suter L,Rüegg M,Zemp N,Hennig L,Widmer A Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. Plant Physiol., 2014. 166(4): p. 1928-42 [PMID:25339407]