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

RrC4371_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

C2H2

Protein Properties

Length: 547aa MW: 59868.5 Da PI: 9.2841

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4371_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.8e-05	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H RrC4371_p1 6 FICEVCNKGFQREQNLQLHRRGH 28 89*******************88 PP
2	zf-C2H2	13.2	0.00026	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ RrC4371_p1 82 WKCEKCSKRYAVQSDWKAHSKTC 104 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.51E-7	5	28	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.0E-6	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	2.7E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.99	6	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0052	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	2.5E-5	70	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.51E-7	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: 547 aa Download sequence Send to blast
MATNRFICEV CNKGFQREQN LQLHRRGHNL PWKLKQKSTK EVRRKVYLCP EPTCVHHDPS 60 RALGDLTGIK KHYYRKHGEK KWKCEKCSKR YAVQSDWKAH SKTCGTKEYR CDCGTLFSRR 120 DSFITHRAFC DALAQESARH PTSLTSLPSH HFPYGQNTNN SNNTSSMILG LSHMGASQNL 180 DHQSSDVLRL GSSGGGGAGA SSRSSSDLIA ANASGYFMQE QNPSFHDQQD HQQQGFLAAS 240 NNIKPSPMNF QQSLMQFSHD NHNSPSSNLF NLSFLSGHNG VASATSNPNA AAVSSGNLMI 300 SNHFDSENAV GGGRGGGERS TGLFPNNLMT SADRISTGAV PSLFSSSMQN PNSTTHMSAT 360 ALLQKAAQIG SSSSNNSNSN NASSILRSFG SGMYGESETN LNDLMNTFSN PGATGNNVNR 420 VDSPFGSYGG VNKGLNADKQ SMTRDFLGVG QIVRSMSGSG GFQQQKQQQR HGNSTEIVGS 480 STDSANINSI NSMSWRVQAA FAKFLCLFVF IFFYLPFYSL RKFFNLFSFV ILTSWQCHEC 540 LSCDLPF

Sequence ? help Back to Top

Protein Sequence Length: 547 aa Download sequence Send to blast

MATNRFICEV CNKGFQREQN LQLHRRGHNL PWKLKQKSTK EVRRKVYLCP EPTCVHHDPS  60
RALGDLTGIK KHYYRKHGEK KWKCEKCSKR YAVQSDWKAH SKTCGTKEYR CDCGTLFSRR  120
DSFITHRAFC DALAQESARH PTSLTSLPSH HFPYGQNTNN SNNTSSMILG LSHMGASQNL  180
DHQSSDVLRL GSSGGGGAGA SSRSSSDLIA ANASGYFMQE QNPSFHDQQD HQQQGFLAAS  240
NNIKPSPMNF QQSLMQFSHD NHNSPSSNLF NLSFLSGHNG VASATSNPNA AAVSSGNLMI  300
SNHFDSENAV GGGRGGGERS TGLFPNNLMT SADRISTGAV PSLFSSSMQN PNSTTHMSAT  360
ALLQKAAQIG SSSSNNSNSN NASSILRSFG SGMYGESETN LNDLMNTFSN PGATGNNVNR  420
VDSPFGSYGG VNKGLNADKQ SMTRDFLGVG QIVRSMSGSG GFQQQKQQQR HGNSTEIVGS  480
STDSANINSI NSMSWRVQAA FAKFLCLFVF IFFYLPFYSL RKFFNLFSFV ILTSWQCHEC  540
LSCDLPF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-34	78	139	3	64	Zinc finger protein JACKDAW
5b3h_F	2e-34	78	139	3	64	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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:22898356, ECO:0000269\|PubMed:24821766}.

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	AJ621495	0.0	AJ621495.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 2 (idz2 gene).
GenBank	AY056174	0.0	AY056174.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBank	AY081314	0.0	AY081314.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBank	BT001215	0.0	BT001215.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018462818.1	0.0	PREDICTED: protein indeterminate-domain 5, chloroplastic-like
Swissprot	Q9ZUL3	0.0	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	M4FIP5	0.0	M4FIP5_BRARP; Uncharacterized protein
STRING	Bra040974.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4373	26	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	0.0	indeterminate(ID)-domain 5

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]