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

GSBRNA2T00030868001

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

C2H2

Protein Properties

Length: 120aa MW: 14099.4 Da PI: 10.3411

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00030868001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.6	1.1e-05	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H GSBRNA2T00030868001 6 FICDVCKKGFQREQNLQLHRRGH 28 89*******************88 PP
2	zf-C2H2	15.9	3.7e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ GSBRNA2T00030868001 82 WKCEKCSKRYAVQSDWKAHSKTC 104 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.8E-8	5	28	No hit	No description
Gene3D	G3DSA:3.30.160.60	8.3E-6	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF13912	1.4E-5	5	28	IPR007087	Zinc finger, C2H2
PROSITE profile	PS50157	10.616	6	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.014	6	28	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	47	77	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.8E-6	70	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.8E-8	77	102	No hit	No description
SMART	SM00355	130	82	102	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 120 aa Download sequence Send to blast
MATNRFICDV CKKGFQREQN LQLHRRGHNL PWKLKQKSTK DVKRKVYLCP EPTCVHHDPS 60 RALGDLTGIK KHYYRKHGEK KWKCEKCSKR YAVQSDWKAH SKTCGTKEYR CDCGTIFSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	8e-22	78	119	3	44	Zinc finger protein JACKDAW
5b3h_F	8e-22	78	119	3	44	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:24821766, ECO:0000305\|PubMed:19726569}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00030868001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

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	HM222924	1e-167	HM222924.1 Thellungiella parvula phosphatase, cyclin J18, clathrin assembly protein-related protein, BPC1, SGR5/ATIDD15, leucine-rich receptor kinase, endomemebrane protein 70, salt overly sensitive 1, glutamate decarboxylae 4, oligopeptide transport protein, peptide transporter, and NADH-ubiquinone oxidoreductase B18 genes, complete cds; and unknown genes.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013691845.1	1e-89	protein indeterminate-domain 4, chloroplastic-like isoform X2
Refseq	XP_013691857.1	1e-89	protein indeterminate-domain 4, chloroplastic-like isoform X2
Refseq	XP_022572232.1	1e-89	protein indeterminate-domain 4, chloroplastic-like isoform X2
Swissprot	Q8GYC1	2e-89	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A3P6B573	1e-87	A0A3P6B573_BRACM; Uncharacterized protein
TrEMBL	E5F711	2e-87	E5F711_9BRAS; Uncharacterized protein
STRING	AT2G02080.1	7e-88	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	6e-92	indeterminate(ID)-domain 4

Publications ? help Back to Top
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]