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

GSBRNA2T00000787001

Common Name

GSBRNA2T00000787001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

MIKC_MADS

Protein Properties

Length: 344aa MW: 39674.7 Da PI: 9.4847

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00000787001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	67	1.9e-21	9	56	1	48
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48 krienks rqvtf+kRrng++ KA LSvLC+ vav+++s tgkly GSBRNA2T00000787001 9 KRIENKSSRQVTFCKRRNGLIEKARQLSVLCESSVAVLVVSATGKLYN 56 79********************************************96 PP
2	K-box	30.3	1.8e-11	247	309	37	99
K-box 37 hllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 +l +++ s+ L++Le+qLe++l+ R++K++l++e +++ ++kek l een L +k+ GSBRNA2T00000787001 247 NLEEANVDGVSVDSLNSLEEQLETALSVTRTTKTKLMMEFLKTRREKEKLLIEENLVLASKVT 309 4555677889999*********************************************99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	27.824	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.5E-31	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.18E-23	1	72	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-22	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.8E-20	10	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-22	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.2E-22	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	10.397	224	314	IPR002487	Transcription factor, K-box
Pfam	PF01486	7.9E-9	251	308	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:0016021	Cellular Component	integral component of membrane
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: 344 aa Download sequence Send to blast
MGRKKVEIKR IENKSSRQVT FCKRRNGLIE KARQLSVLCE SSVAVLVVSA TGKLYNSSSG 60 DKLNNVVAKI YMFLVFVLFC HFVIMIFIFS INCTNFILIL HVIPEKNLHV LIRAQCCLMV 120 ETCFQMGRTG PRPSRMKHSP QVPNFFETLY IHKPPNLSKE KRINWDIEVL TFPEMLNPLS 180 CLTLYGVSPI FQPKIYTKIF LNRPIVLSKI IDRYKIQQAD DLQTLDLEEI TRNYLPHKKL 240 LELVQSNLEE ANVDGVSVDS LNSLEEQLET ALSVTRTTKT KLMMEFLKTR REKEKLLIEE 300 NLVLASKVTE IWKQTFLVTR DETSMLPEYR FGNNPPETLS LLK*

Sequence ? help Back to Top

Protein Sequence Length: 344 aa Download sequence Send to blast

MGRKKVEIKR IENKSSRQVT FCKRRNGLIE KARQLSVLCE SSVAVLVVSA TGKLYNSSSG  60
DKLNNVVAKI YMFLVFVLFC HFVIMIFIFS INCTNFILIL HVIPEKNLHV LIRAQCCLMV  120
ETCFQMGRTG PRPSRMKHSP QVPNFFETLY IHKPPNLSKE KRINWDIEVL TFPEMLNPLS  180
CLTLYGVSPI FQPKIYTKIF LNRPIVLSKI IDRYKIQQAD DLQTLDLEEI TRNYLPHKKL  240
LELVQSNLEE ANVDGVSVDS LNSLEEQLET ALSVTRTTKT KLMMEFLKTR REKEKLLIEE  300
NLVLASKVTE IWKQTFLVTR DETSMLPEYR FGNNPPETLS LLK*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.23611	0.0	seed\| vegetative meristem

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	GSBRNA2T00000787001

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009150584.1	1e-89	PREDICTED: agamous-like MADS-box protein AGL27 isoform X1
Refseq	XP_013643102.1	1e-89	agamous-like MADS-box protein AGL27 isoform X1
Swissprot	Q9LSR7	4e-49	AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBL	A0A078F2T1	0.0	A0A078F2T1_BRANA; BnaA06g23990D protein
STRING	Bo3g100570.1	7e-98	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM986	19	87

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G65060.1	2e-51	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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]