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

GSBRNA2T00095586001

Common Name

GSBRNA2T00095586001

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: 479aa MW: 51822.5 Da PI: 9.0849

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00095586001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15	7.2e-05	62	84	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H GSBRNA2T00095586001 62 FICDVCKKGFQREQNLQLHRRGH 84 89*******************88 PP
2	zf-C2H2	12.8	0.00035	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k++ +s+ k H +t+ GSBRNA2T00095586001 138 WKCDKCSKRYAVQSDWKAHSKTC 160 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF13912	9.3E-5	61	84	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	5.8E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.18E-7	61	84	No hit	No description
SMART	SM00355	0.014	62	84	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.616	62	84	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	103	133	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.0E-5	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.18E-7	133	158	No hit	No description
SMART	SM00355	140	138	158	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: 479 aa Download sequence Send to blast
MASSSYNASV VPSSSSSAQP FFLTGSGLHH PRNEETNPET QANPDAEVVA LSPKTIMATN 60 RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR KVYLCPEPTC VHHDPSRALG 120 DLTGIKKHYY RKHGEKKWKC DKCSKRYAVQ SDWKAHSKTC GTKEYRCDCG TIFSRRDSYI 180 THRAFCDALI QETARNPTLS FTSMEAASSG AGSGGLYGRL DGGRTLSHHH LSGHPNSGFS 240 PLAGYNLNIA SSENSRHFVP QTSNPNFLIQ SSQGMLTVPN NNDQSFMNHQ GLNQFDPVNN 300 INSKSSTNNS FFNLGFFQEN IKNSETSLPS LYSSDVLVHH PEESLNVGSN VSATALLQKA 360 TQMGSITSND PSALLRGLAS SSSNDFGGGQ IMGNDNNGNL QGLMNSLVAV NGGGAGGSGG 420 NIFDVHFGNN GNMSGSDKLT LDFLGVGGMV RNVNRGRGRG GDVGELKFSE QNHPFGRS*

Sequence ? help Back to Top

Protein Sequence Length: 479 aa Download sequence Send to blast

MASSSYNASV VPSSSSSAQP FFLTGSGLHH PRNEETNPET QANPDAEVVA LSPKTIMATN  60
RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR KVYLCPEPTC VHHDPSRALG  120
DLTGIKKHYY RKHGEKKWKC DKCSKRYAVQ SDWKAHSKTC GTKEYRCDCG TIFSRRDSYI  180
THRAFCDALI QETARNPTLS FTSMEAASSG AGSGGLYGRL DGGRTLSHHH LSGHPNSGFS  240
PLAGYNLNIA SSENSRHFVP QTSNPNFLIQ SSQGMLTVPN NNDQSFMNHQ GLNQFDPVNN  300
INSKSSTNNS FFNLGFFQEN IKNSETSLPS LYSSDVLVHH PEESLNVGSN VSATALLQKA  360
TQMGSITSND PSALLRGLAS SSSNDFGGGQ IMGNDNNGNL QGLMNSLVAV NGGGAGGSGG  420
NIFDVHFGNN GNMSGSDKLT LDFLGVGGMV RNVNRGRGRG GDVGELKFSE QNHPFGRS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	7e-34	134	200	3	69	Zinc finger protein JACKDAW
5b3h_F	7e-34	134	200	3	69	Zinc finger protein JACKDAW
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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	GSBRNA2T00095586001

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	AK117733	0.0	AK117733.1 Arabidopsis thaliana At2g02080 mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL17-41-L01.
GenBank	BT005897	0.0	BT005897.1 Arabidopsis thaliana At2g02080 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013714783.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A078FSD5	0.0	A0A078FSD5_BRANA; BnaC09g20970D protein
STRING	Bo9g071570.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3678	17	59

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	0.0	indeterminate(ID)-domain 4

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