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

GSBRNA2T00048692001

Common Name

GSBRNA2T00048692001, GSBRNA2T00072693001

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

M-type_MADS

Protein Properties

Length: 70aa MW: 7825.1 Da PI: 10.5644

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00048692001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	96.8	9.2e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++ klye+ss GSBRNA2T00048692001 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPSSKLYEFSS 59 79***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	31.413	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	4.4E-40	1	60	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
CDD	cd00265	5.94E-38	3	66	No hit	No description
PRINTS	PR00404	6.1E-31	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	2.49E-30	3	65	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.3E-27	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.1E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.1E-31	38	59	IPR002100	Transcription factor, MADS-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:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 70 aa Download sequence Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP SSKLYEFSSS 60 GQERLITIN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3mu6_A	9e-20	3	66	2	65	Myocyte-specific enhancer factor 2A
3mu6_B	9e-20	3	66	2	65	Myocyte-specific enhancer factor 2A
3mu6_C	9e-20	3	66	2	65	Myocyte-specific enhancer factor 2A
3mu6_D	9e-20	3	66	2	65	Myocyte-specific enhancer factor 2A
6byy_A	1e-19	1	66	1	66	MEF2 CHIMERA
6byy_B	1e-19	1	66	1	66	MEF2 CHIMERA
6byy_C	1e-19	1	66	1	66	MEF2 CHIMERA
6byy_D	1e-19	1	66	1	66	MEF2 CHIMERA
6bz1_A	1e-19	1	66	1	66	MEF2 CHIMERA
6bz1_B	1e-19	1	66	1	66	MEF2 CHIMERA
6bz1_C	1e-19	1	66	1	66	MEF2 CHIMERA
6bz1_D	1e-19	1	66	1	66	MEF2 CHIMERA
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Mostly expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. Also present in rosette leaves and seedlings and, to a lesser extent, in cauline leaves and flowers. Enriched in apices including the shoot apical meristem and developing leaf primordia. {ECO:0000269\|PubMed:11115127, ECO:0000269\|PubMed:12837945, ECO:0000269\|PubMed:12949148, ECO:0000269\|PubMed:16778081}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00048692001

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	7e-62	AK230464.1 Arabidopsis thaliana mRNA for MADS-box protein AGL14, complete cds, clone: RAFL26-03-G06.
GenBank	AL078606	7e-62	AL078606.1 Arabidopsis thaliana DNA chromosome 4, BAC clone T26M18 (ESSA project).
GenBank	AL161532	7e-62	AL161532.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 32.
GenBank	AL161533	7e-62	AL161533.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 33.
GenBank	CP002687	7e-62	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018444499.1	5e-36	PREDICTED: agamous-like MADS-box protein AGL19
Refseq	XP_022549659.1	1e-36	agamous-like MADS-box protein AGL19
Swissprot	O82743	6e-35	AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBL	A0A078HWX3	5e-42	A0A078HWX3_BRANA; BnaA01g12710D protein
STRING	Bo1g031900.1	3e-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
AT4G22950.1	3e-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] 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]