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

GSVIVT01025166001

Common Name

VIT_06s0004g03070

Organism

Vitis vinifera

Taxonomic ID

29760

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis

Family

C2H2

Protein Properties

Length: 478aa MW: 52536 Da PI: 9.6539

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSVIVT01025166001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.2	2.9e-05	62	84	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H GSVIVT01025166001 62 FICEICNKGFQRDQNLQLHRRGH 84 89*******************88 PP
2	zf-C2H2	12	0.00067	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H + + GSVIVT01025166001 138 WKCEKCSKKYAVQSDWKAHSKIC 160 58*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.3E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.82E-7	61	84	No hit	No description
PROSITE profile	PS50157	10.845	62	84	IPR007087	Zinc finger, C2H2
Pfam	PF12171	5.7E-5	62	84	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.022	62	84	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	91	103	133	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.0E-5	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.82E-7	133	158	No hit	No description
SMART	SM00355	140	138	158	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: 478 aa Download sequence Send to blast
MAEDGLTLPS SIRGFVQEPN SNPNPNPSAN PVKKKRNLPG TPDPEAEVIA LSPKSLMATN 60 RFICEICNKG FQRDQNLQLH RRGHNLPWKL RQRTSKEVRK KVYICPEKSC VHHNPTRALG 120 DLTGIKKHYS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKIC GTREYKCDCG TLFSRKDSFI 180 THRAFCDALA EESARLTSVS APNPIFRNEL MNGSISNPQA HIIPQFSSPR LPLWLDHANS 240 HLNNPIGVNT NGSFLAPTSA GLPEMVQTAP MSMYGSPASS QNQWLQRCSE ASFTSSTLPR 300 VLKEEEENKG NLSESITSLF SSNQNQQESS AHMSATALLQ KAAQMGSTKS NSAFFSTTGF 360 GSINSSLSNT TPFSSYPHGR SNNQVHKFLI RQSNQSDSMN QLINSTSPSS TMGDGLLMGD 420 MNSTPLFHAS SNEVERGLTR DFLGVGSDAS RPFLQQELAK FASMGSAMGM SQYSGNH*

Sequence ? help Back to Top

Protein Sequence Length: 478 aa Download sequence Send to blast

MAEDGLTLPS SIRGFVQEPN SNPNPNPSAN PVKKKRNLPG TPDPEAEVIA LSPKSLMATN  60
RFICEICNKG FQRDQNLQLH RRGHNLPWKL RQRTSKEVRK KVYICPEKSC VHHNPTRALG  120
DLTGIKKHYS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKIC GTREYKCDCG TLFSRKDSFI  180
THRAFCDALA EESARLTSVS APNPIFRNEL MNGSISNPQA HIIPQFSSPR LPLWLDHANS  240
HLNNPIGVNT NGSFLAPTSA GLPEMVQTAP MSMYGSPASS QNQWLQRCSE ASFTSSTLPR  300
VLKEEEENKG NLSESITSLF SSNQNQQESS AHMSATALLQ KAAQMGSTKS NSAFFSTTGF  360
GSINSSLSNT TPFSSYPHGR SNNQVHKFLI RQSNQSDSMN QLINSTSPSS TMGDGLLMGD  420
MNSTPLFHAS SNEVERGLTR DFLGVGSDAS RPFLQQELAK FASMGSAMGM SQYSGNH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-38	134	203	3	72	Zinc finger protein JACKDAW
5b3h_F	2e-38	134	203	3	72	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	88	100	KLRQRTSKEVRKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Vvi.3360	0.0	bud\| fruit

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269\|PubMed:17785527}.
Uniprot	TISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269\|PubMed:17785527}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

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	AM451995	0.0	AM451995.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X227225.4, clone ENTAV 115.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002282251.2	0.0	PREDICTED: protein indeterminate-domain 9
Swissprot	Q700D2	1e-124	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	F6GTZ5	0.0	F6GTZ5_VITVI; Uncharacterized protein
STRING	VIT_06s0004g03070.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-113	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	GSVIVT01025166001

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] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]