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

XP_013615577.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

M-type_MADS

Protein Properties

Length: 88aa MW: 9858.33 Da PI: 10.3562

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013615577.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	46.6	4.5e-15	9	45	1	37
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevav 37 k ienks rq tfskRr+g++ KA LSvLC+ vav XP_013615577.1 9 KLIENKSSRQDTFSKRRTGLIEKARQLSVLCESSVAV 45 569********************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	21.572	1	51	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	2.88E-18	1	53	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.1E-18	1	60	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-14	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	7.9E-15	11	45	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-14	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-14	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: 88 aa Download sequence Send to blast
MGRRKVEIKL IENKSSRQDT FSKRRTGLIE KARQLSVLCE SSVAVPALEN STTPLPVTNT 60 VYSIVMHFRR IAERLIGVNG DTDQESLA

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Mostly expressed in roots, leaves and flowers, and, to a lower extent, in inflorescence, siliques, pollen and shoots. {ECO:0000269\|PubMed:12837945, ECO:0000269\|PubMed:12949148}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the negative regulation of flowering time, probably through the photoperiodic and vernalization pathways; more efficient in cv. Landsberg erecta than in cv. Columbia background. Prevents premature flowering (PubMed:12724541, PubMed:25339407). Involved in the modulation of vernalization impact on flowering according to genotype acclimation to altitude (PubMed:25339407). {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:25339407}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013615577.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed during vernalization (PubMed:12724541). Regulated by HAM1 and HAM2 via epigenetic modification of chromatins at H4K5 acetylation during flowering (PubMed:23273925). {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:23273925}.

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	4e-67	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_013615577.1	8e-59	PREDICTED: agamous-like MADS-box protein AGL31 isoform X1
Swissprot	Q9LSR7	2e-20	AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBL	A0A0D2ZWV1	2e-57	A0A0D2ZWV1_BRAOL; Uncharacterized protein
STRING	Bo03856s010.1	3e-58	(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
AT5G65060.2	6e-23	MIKC_MADS family protein

Publications ? help Back to Top
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] 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] Nasim Z,Fahim M,Ahn JH Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay. Front Plant Sci, 2017. 8: p. 191 [PMID:28261246]