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

GSBRNA2T00090140001

Common Name

GSBRNA2T00090140001

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: 474aa MW: 51855.5 Da PI: 9.0961

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00090140001	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	7.1e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H GSBRNA2T00090140001 82 FICDVCKKGFQREQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	13.5	0.00022	158	180	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ GSBRNA2T00090140001 158 WKCEKCSKRYAVQSDWKAHSKTC 180 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.93E-7	81	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.7E-5	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.014	82	104	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.616	82	104	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	84	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	123	153	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.0E-5	146	179	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.93E-7	153	178	No hit	No description
SMART	SM00355	130	158	178	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: 474 aa Download sequence Send to blast
MSSSSYNASV APSSSSAEPF FLTGSGVRDN EFDRKDTFIS MIQEPNSSAQ PPKKRRNQPG 60 NPNPDAEVVA LSPKTLMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKDVKR 120 KVYLCPEPTC VHHDPSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC 180 GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARIPTVS FTSMASASSG AVSGGFYRRL 240 DGGNALAHHN LNDHHNSGFS PIPGYNLNIA STENSRDYVQ QTSDPNFLIQ CSSSQRMLTV 300 PNNNDQSFMN EQGMIQFDPV NNTNLKSNTN NSFFNLGFFQ ENTKNSETSL PSLYSTDVHT 360 LTSNDPSAFF RGLASSSNSS SMVGNDFGGG QIMGNNNNGS LQGLMSSLVA VNGGGAAGSG 420 GNIFDVHFGN IENMSGSNKL TLDFLGVGGL VRNVNRGGGH GDVPEQNHTF GRP*

Sequence ? help Back to Top

Protein Sequence Length: 474 aa Download sequence Send to blast

MSSSSYNASV APSSSSAEPF FLTGSGVRDN EFDRKDTFIS MIQEPNSSAQ PPKKRRNQPG  60
NPNPDAEVVA LSPKTLMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKDVKR  120
KVYLCPEPTC VHHDPSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC  180
GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARIPTVS FTSMASASSG AVSGGFYRRL  240
DGGNALAHHN LNDHHNSGFS PIPGYNLNIA STENSRDYVQ QTSDPNFLIQ CSSSQRMLTV  300
PNNNDQSFMN EQGMIQFDPV NNTNLKSNTN NSFFNLGFFQ ENTKNSETSL PSLYSTDVHT  360
LTSNDPSAFF RGLASSSNSS SMVGNDFGGG QIMGNNNNGS LQGLMSSLVA VNGGGAAGSG  420
GNIFDVHFGN IENMSGSNKL TLDFLGVGGL VRNVNRGGGH GDVPEQNHTF GRP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-35	154	220	3	69	Zinc finger protein JACKDAW
5b3h_F	6e-35	154	220	3	69	Zinc finger protein JACKDAW
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.17150	1e-164	seed

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	GSBRNA2T00090140001

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013693621.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_022552723.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_022552724.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A078FSD0	0.0	A0A078FSD0_BRANA; BnaC02g34330D protein
STRING	Bra026616.1-P	0.0	(Brassica rapa)

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]