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

XP_009101275.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 506aa MW: 54882.7 Da PI: 9.4953

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009101275.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.9	7.7e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H XP_009101275.1 82 FICDVCKKGFQREQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	12.7	0.00037	158	180	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k++ +s+ k H +t+ XP_009101275.1 158 WKCDKCSKRYAVQSDWKAHSKTC 180 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF13912	1.0E-4	81	104	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.38E-7	81	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.2E-5	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.616	82	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.014	82	104	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	84	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	65	123	153	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.1E-5	145	179	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.38E-7	153	178	No hit	No description
SMART	SM00355	140	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: 506 aa Download sequence Send to blast
MSSSSYNTSV VPSSSSTQPF FITGSSAGDN AFDRKDTFMS MVQQPNSSAP QPKKRRNQPG 60 NPNPDAEVAA LSPTTQMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR 120 KVYICPEPTC VHHDPARALG DLTGVKKHYY RKHGEKKWKC DKCSKRYAVQ SDWKAHSKTC 180 GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARNPTVS FTSMTAASSG AGFRGFHGRL 240 EGGNALSHHH LSDHPNSGFS SFGGYNLNIA SSENSRDFAP QTSNPNFLVQ SQGMLTQPNN 300 NNNDQSFMNQ QGLIQFDPVN NINLKSSTTN NSFFNLGFFQ ENTKNSETAI PSLYSTDSLV 360 HHREESLNAG SNVSATALLQ KATQLGSITS NDPSALFRGL ASSSNSSSVV VNDFGGGQIM 420 GNDNNGNLQG LMNSLVAVNG GGAGGSGGNI FNVDFGNNNV NMSGSDNLTL DFLGVGGMVR 480 NVNRGGAGRG RVRGDVSLNG ELKFPE

Sequence ? help Back to Top

Protein Sequence Length: 506 aa Download sequence Send to blast

MSSSSYNTSV VPSSSSTQPF FITGSSAGDN AFDRKDTFMS MVQQPNSSAP QPKKRRNQPG  60
NPNPDAEVAA LSPTTQMATN RFICDVCKKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR  120
KVYICPEPTC VHHDPARALG DLTGVKKHYY RKHGEKKWKC DKCSKRYAVQ SDWKAHSKTC  180
GTKEYRCDCG TIFSRRDSYI THRAFCDALI QETARNPTVS FTSMTAASSG AGFRGFHGRL  240
EGGNALSHHH LSDHPNSGFS SFGGYNLNIA SSENSRDFAP QTSNPNFLVQ SQGMLTQPNN  300
NNNDQSFMNQ QGLIQFDPVN NINLKSSTTN NSFFNLGFFQ ENTKNSETAI PSLYSTDSLV  360
HHREESLNAG SNVSATALLQ KATQLGSITS NDPSALFRGL ASSSNSSSVV VNDFGGGQIM  420
GNDNNGNLQG LMNSLVAVNG GGAGGSGGNI FNVDFGNNNV NMSGSDNLTL DFLGVGGMVR  480
NVNRGGAGRG RVRGDVSLNG ELKFPE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-33	154	220	3	69	Zinc finger protein JACKDAW
5b3h_F	4e-33	154	220	3	69	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00256	DAP	Transfer from AT2G02080	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009101275.1

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	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_009101274.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic
Refseq	XP_009101275.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A397Z3I7	0.0	A0A397Z3I7_BRACM; Uncharacterized protein
STRING	Bo7g080200.1	0.0	(Brassica oleracea)

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