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_03805.1_g00003.1

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: 194aa MW: 22194.4 Da PI: 10.2781

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_03805.1_g00003.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	18.1	7.3e-06	81	103	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Rsa1.0_03805.1_g00003.1 81 FICEVCNKGFQREQNLQLHRRGH 103 89*******************88 PP
2	zf-C2H2	15.1	6.8e-05	157	179	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Rsa1.0_03805.1_g00003.1 157 WKCEKCSKRYAVQSDWKAHSKTC 179 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.6E-6	80	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.52E-8	80	103	No hit	No description
SMART	SM00355	0.0052	81	103	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	7.0E-6	81	103	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.99	81	103	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	83	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	122	152	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	7.1E-6	145	178	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.52E-8	152	177	No hit	No description
SMART	SM00355	130	157	177	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: 194 aa Download sequence Send to blast
MAASSSSSAS FFGVREDDQS HLLPLNPPAT VPPPPHHQPL QSQQPLEAPP QKKKRNQPRT 60 PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK 120 VYLCPEPTCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCE KCSKRYAVQS DWKAHSKTCG 180 TKEYRCDCGT LFSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-22	153	194	3	44	Zinc finger protein JACKDAW
5b3h_F	1e-22	153	194	3	44	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_03805.1_g00003.1

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	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_018434643.1	1e-145	PREDICTED: protein indeterminate-domain 5, chloroplastic-like
Swissprot	Q9ZUL3	1e-110	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A0D3E7J0	1e-125	A0A0D3E7J0_BRAOL; Uncharacterized protein
STRING	Bo9g071560.1	1e-126	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-109	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]