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

Rsa1.0_01048.1_g00002.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 485aa MW: 52766.6 Da PI: 9.5733

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01048.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15	7.3e-05	67	89	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H Rsa1.0_01048.1_g00002.1 67 FICDVCKKGFQREQNLQLHRRGH 89 89*******************88 PP
2	zf-C2H2	13.4	0.00022	143	165	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Rsa1.0_01048.1_g00002.1 143 WKCEKCSKRYAVQSDWKAHSKTC 165 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.99E-7	67	89	No hit	No description
SMART	SM00355	0.014	67	89	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.4E-4	67	89	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.616	67	89	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	69	89	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	108	138	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.1E-5	131	164	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.99E-7	138	163	No hit	No description
SMART	SM00355	130	143	163	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: 485 aa Download sequence Send to blast
MASSSSYNAS VVPSSSSSVQ PLFLTGSGVG ESDFDQKDTF MSIIQQPNSS APPPKKRRNQ 60 PGNPSKFICD VCKKGFQREQ NLQLHRRGHN LPWKLKQKST KEVKRKVYLC PEPTCVHHDP 120 SRALGDLTGI KKHYYRKHGE KKWKCEKCSK RYAVQSDWKA HSKTCGTKEY RCDCGTIFSR 180 RDSYITHRAF CDALIQETGR NPTMSFTSIA AASSGAGSGV FYGRLDGGRT LSHHHLSDHP 240 NSGFPPLAGY NLNMASSENS RHFVPQTSNP NFLIQSSQGM LTLPNNSDQS FMNQQGLNQF 300 DPLNNINSKS STNNSFFNLG FFQENTKNSE TSLPSLYRSD VLVHHPGESL NVGSNVSATA 360 LLQKATQMGS ITSNDPSALF RGLASSSSND FGEGQIMGND NNGNLQGLMN SLVAANGGGA 420 GGSGGNIFDV HFGNNANMSG SDKLTLDFLG VGGMVRNVNR GRGRGDVSLD GDLKFSEQNH 480 PFGRS

Sequence ? help Back to Top

Protein Sequence Length: 485 aa Download sequence Send to blast

MASSSSYNAS VVPSSSSSVQ PLFLTGSGVG ESDFDQKDTF MSIIQQPNSS APPPKKRRNQ  60
PGNPSKFICD VCKKGFQREQ NLQLHRRGHN LPWKLKQKST KEVKRKVYLC PEPTCVHHDP  120
SRALGDLTGI KKHYYRKHGE KKWKCEKCSK RYAVQSDWKA HSKTCGTKEY RCDCGTIFSR  180
RDSYITHRAF CDALIQETGR NPTMSFTSIA AASSGAGSGV FYGRLDGGRT LSHHHLSDHP  240
NSGFPPLAGY NLNMASSENS RHFVPQTSNP NFLIQSSQGM LTLPNNSDQS FMNQQGLNQF  300
DPLNNINSKS STNNSFFNLG FFQENTKNSE TSLPSLYRSD VLVHHPGESL NVGSNVSATA  360
LLQKATQMGS ITSNDPSALF RGLASSSSND FGEGQIMGND NNGNLQGLMN SLVAANGGGA  420
GGSGGNIFDV HFGNNANMSG SDKLTLDFLG VGGMVRNVNR GRGRGDVSLD GDLKFSEQNH  480
PFGRS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-33	139	205	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-33	139	205	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01048.1_g00002.1

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	-

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_018462817.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A397XWE2	0.0	A0A397XWE2_BRACM; Uncharacterized 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
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]