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

GSBRNA2T00001822001

Common Name

GSBRNA2T00001822001

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: 514aa MW: 55622.5 Da PI: 9.2331

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00001822001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.9	7.8e-05	89	111	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H GSBRNA2T00001822001 89 FICDVCKKGFQREQNLQLHRRGH 111 89*******************88 PP
2	zf-C2H2	12.7	0.00038	165	187	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k++ +s+ k H +t+ GSBRNA2T00001822001 165 WKCDKCSKRYAVQSDWKAHSKTC 187 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.3E-7	88	111	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.3E-5	88	111	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF13912	1.0E-4	88	111	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.014	89	111	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.616	89	111	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	91	111	IPR007087	Zinc finger, C2H2
SMART	SM00355	65	130	160	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.2E-5	152	186	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.3E-7	160	185	No hit	No description
SMART	SM00355	140	165	185	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: 514 aa Download sequence Send to blast
MSSSSYNTSV VPSSSSTQPF FITGSSAGDN AFDRKDTFMS MVQQPNSSAP QPKKRRNQPG 60 NPSNLIDQSD PDAEVVALSP TTLMATNRFI CDVCKKGFQR EQNLQLHRRG HNLPWKLKQK 120 STKEVKRKVY ICPEPTCVHH DPARALGDLT GVKKHYYRKH GEKKWKCDKC SKRYAVQSDW 180 KAHSKTCGTK EYRCDCGTIF SRRDSYITHR AFCDALIQET ARNPTVSFTS VTAASSGAGF 240 RGFHGRLEGG NALSHHHLSD HPNSGFSSFG GYNLNIASSE NSRDFAPQTS NPNFLVQSQG 300 MLTQPNNNNN DQSFMNQQGL IQFDPVNNIN LKSSTTNNSF FNLGFFQENT KNSETAIPSL 360 YSTDSLVHHR EESLNAGSNV SATALLQKAT QLGSITSNDP SALFRGLASS SNSSSVVVND 420 FGGGQIMGND NNGNLQGLMN SLVAVNGGGA GGSGGNIFNV DFGNNNVNMS GSDNLTLDFL 480 GVGGMVRNVN RGGAGRGRVR GDVSLNGELK FPE*

Sequence ? help Back to Top

Protein Sequence Length: 514 aa Download sequence Send to blast

MSSSSYNTSV VPSSSSTQPF FITGSSAGDN AFDRKDTFMS MVQQPNSSAP QPKKRRNQPG  60
NPSNLIDQSD PDAEVVALSP TTLMATNRFI CDVCKKGFQR EQNLQLHRRG HNLPWKLKQK  120
STKEVKRKVY ICPEPTCVHH DPARALGDLT GVKKHYYRKH GEKKWKCDKC SKRYAVQSDW  180
KAHSKTCGTK EYRCDCGTIF SRRDSYITHR AFCDALIQET ARNPTVSFTS VTAASSGAGF  240
RGFHGRLEGG NALSHHHLSD HPNSGFSSFG GYNLNIASSE NSRDFAPQTS NPNFLVQSQG  300
MLTQPNNNNN DQSFMNQQGL IQFDPVNNIN LKSSTTNNSF FNLGFFQENT KNSETAIPSL  360
YSTDSLVHHR EESLNAGSNV SATALLQKAT QLGSITSNDP SALFRGLASS SNSSSVVVND  420
FGGGQIMGND NNGNLQGLMN SLVAVNGGGA GGSGGNIFNV DFGNNNVNMS GSDNLTLDFL  480
GVGGMVRNVN RGGAGRGRVR GDVSLNGELK FPE*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-33	161	227	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-33	161	227	3	69	Zinc finger protein JACKDAW
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.1685	0.0	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	GSBRNA2T00001822001

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_013599228.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599229.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599230.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599231.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599232.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599233.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013599234.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013736158.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013736159.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013736160.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_013736161.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_022560774.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Refseq	XP_022560776.1	0.0	protein indeterminate-domain 4, chloroplastic-like
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A078FWX9	0.0	A0A078FWX9_BRANA; BnaA06g34330D protein
STRING	Bra024833.1-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]