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

GSBRNA2T00094672001

Common Name

GSBRNA2T00094672001, LOC106366094

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: 194aa MW: 22835.2 Da PI: 9.8544

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00094672001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	94.3	5.4e-30	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+ien + rqvtfskRrng+lKKA+ELSvLCda+v++i+fs++g+lye+ss GSBRNA2T00094672001 9 KKIENATSRQVTFSKRRNGLLKKAYELSVLCDAQVSLIVFSQRGRLYEFSS 59 68***********************************************96 PP
2	K-box	67	6.4e-23	77	170	4	97
K-box 4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 ++++ +e ++l+qe++ + ++ie L+ +R+llG++L+s+sl+eLq++ +qL++sl ++R++K ++++eq+e+l+ kek+l een + GSBRNA2T00094672001 77 ETSNQYSEMYIQQLKQEASHMIAKIELLEFHKRKLLGQELSSCSLQELQEIDSQLQRSLGEVRARKAQMFKEQLEKLKAKEKQLLEENVQ 166 44555788899****************999****************************************************** PP K-box 94 Lrkk 97 L++k GSBRNA2T00094672001 167 LHQK 170 98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	32.352	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	7.5E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.4E-31	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	8.11E-34	3	86	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.06E-42	3	78	No hit	No description
Pfam	PF00319	5.1E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.4E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.4E-31	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	13.089	87	186	IPR002487	Transcription factor, K-box
Pfam	PF01486	2.0E-22	87	170	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: 194 aa Download sequence Send to blast
MVRGKIEMKK IENATSRQVT FSKRRNGLLK KAYELSVLCD AQVSLIVFSQ RGRLYEFSSS 60 DMQNTIERYH TYRNDHETSN QYSEMYIQQL KQEASHMIAK IELLEFHKRK LLGQELSSCS 120 LQELQEIDSQ LQRSLGEVRA RKAQMFKEQL EKLKAKEKQL LEENVQLHQK NVIDPWRGSI 180 DQQKKFRVID LNL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
1tqe_Q	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
1tqe_R	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
1tqe_S	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_A	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_B	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_C	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_D	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_E	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
6c9l_F	9e-21	1	78	1	78	Myocyte-specific enhancer factor 2B
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the shoot apical meristem (SAM) during the vegetative phase and the floral transition. After floral transition, expressed in apical meristem (AM), inflorescence meristem (IM) and floral primordia. {ECO:0000269\|PubMed:21609362}.
Uniprot	TISSUE SPECIFICITY: Expressed in quiescent center (QC) cells of root tips (PubMed:18162590, PubMed:21689171). Expressed at the base of the petiole of cotyledons and leaves, in flower buds, petals, sepals and abscission zone of flowers and siliques. {ECO:0000269\|PubMed:18162590, ECO:0000269\|PubMed:21689171}.

Functional Description ? help Back to Top
Source	Description
UniProt	MADS-box transcription factor that acts with AGL71 and AGL72 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 (PubMed:21609362). Plays a role in controlling flower organ senescence and abscission by repressing ethylene responses and regulating the expression of BOP2 and IDA (PubMed:21689171). {ECO:0000269\|PubMed:21609362, ECO:0000269\|PubMed:21689171}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00094672001

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	AY054220	0.0	AY054220.1 Arabidopsis thaliana At2g45660/F17K2.19 mRNA, complete cds.
GenBank	AY065206	0.0	AY065206.1 Arabidopsis thaliana unknown protein (At5g62165) mRNA, complete cds.
GenBank	AY066035	0.0	AY066035.1 Arabidopsis thaliana At2g45660/F17K2.19 mRNA, complete cds.
GenBank	AY096509	0.0	AY096509.1 Arabidopsis thaliana unknown protein (At5g62165) mRNA, complete cds.
GenBank	AY141213	0.0	AY141213.1 Arabidopsis thaliana MADS-box protein AGL42 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009112008.1	1e-139	PREDICTED: MADS-box protein AGL42-like
Refseq	XP_013661108.1	1e-139	MADS-box protein AGL42 isoform X1
Swissprot	Q9FIS1	1e-116	AGL42_ARATH; MADS-box protein AGL42
TrEMBL	A0A078FVH4	1e-138	A0A078FVH4_BRANA; BnaA09g05900D protein
TrEMBL	A0A3P5Y8H8	1e-138	A0A3P5Y8H8_BRACM; Uncharacterized protein
TrEMBL	M4F4A7	1e-137	M4F4A7_BRARP; Uncharacterized protein
STRING	Bra035907.1-P	1e-138	(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
AT5G62165.3	1e-105	AGAMOUS-like 42

Link Out ? help Back to Top
Entrez Gene	106366094

Publications ? help Back to Top
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]