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

Achn351451

Organism

Actinidia chinensis

Taxonomic ID

3625

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Actinidiaceae; Actinidia

Family

C2H2

Protein Properties

Length: 548aa MW: 60091.7 Da PI: 10.125

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Achn351451	genome	IKGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16	3.4e-05	109	131	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Achn351451 109 FICEICNKGFQRDQNLQLHRRGH 131 89*******************88 PP
2	zf-C2H2	12	0.00065	186	208	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k + +s+ k H +t+ Achn351451 186 WKCDKCSKKYAVQSDWKAHSKTC 208 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.76E-7	108	131	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.5E-5	108	131	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.022	109	131	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	6.7E-5	109	131	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.845	109	131	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	111	131	IPR007087	Zinc finger, C2H2
SMART	SM00355	140	151	181	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.9E-4	173	207	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.76E-7	181	206	No hit	No description
SMART	SM00355	150	186	206	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010075	Biological Process	regulation of meristem growth
GO:0045604	Biological Process	regulation of epidermal cell differentiation
GO:0048364	Biological Process	root development
GO:0051302	Biological Process	regulation of cell division
GO:0003676	Molecular Function	nucleic acid binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 548 aa Download sequence Send to blast
MNILFAPIGV TVQIMRCNSF NQRMNAHSCM QKRERERQRE RQKWPSLNLR LTDFENKGFG 60 QQADPNPNPN PKPITNTVSK KKRNLPGTPD PDAEVIALSP KSLMATNRFI CEICNKGFQR 120 DQNLQLHRRG HNLPWKLKQR ANKDQVRKKV YICPEKACVH HDPARALGDL TGVKKHFSRK 180 HGEKKWKCDK CSKKYAVQSD WKAHSKTCGT REYKCDCGTL FSRKDSFITH RAFCDALAEE 240 SARFTSVAAP TTTMNFRSES NLNEGFNNNN NITQPNLTDG IVGISQFGGG FGPNYGGVAA 300 ANSLISEQQK PGLSLWLDQA NSQLNAIGST SSLPDELQMP PSNLFNSSTM ANFGTLNQSQ 360 WVDKINVATS KSANLYSDNQ NYHPNSPVPP MSATALLQKA AQMGSTRSNP SFTGNNFGLM 420 NSNINNAVSH GRNDQSHHLV GHKQASEILV GPANLPARDS LMGSSSLSSV TSATSSNIEQ 480 IMMQSGVNSI VPLKLHPGSN RIENGLTRDF LGMGGEGSGR AFLPQELAKF ASMGSAMGLS 540 HFNTSSH*

Sequence ? help Back to Top

Protein Sequence Length: 548 aa Download sequence Send to blast

MNILFAPIGV TVQIMRCNSF NQRMNAHSCM QKRERERQRE RQKWPSLNLR LTDFENKGFG  60
QQADPNPNPN PKPITNTVSK KKRNLPGTPD PDAEVIALSP KSLMATNRFI CEICNKGFQR  120
DQNLQLHRRG HNLPWKLKQR ANKDQVRKKV YICPEKACVH HDPARALGDL TGVKKHFSRK  180
HGEKKWKCDK CSKKYAVQSD WKAHSKTCGT REYKCDCGTL FSRKDSFITH RAFCDALAEE  240
SARFTSVAAP TTTMNFRSES NLNEGFNNNN NITQPNLTDG IVGISQFGGG FGPNYGGVAA  300
ANSLISEQQK PGLSLWLDQA NSQLNAIGST SSLPDELQMP PSNLFNSSTM ANFGTLNQSQ  360
WVDKINVATS KSANLYSDNQ NYHPNSPVPP MSATALLQKA AQMGSTRSNP SFTGNNFGLM  420
NSNINNAVSH GRNDQSHHLV GHKQASEILV GPANLPARDS LMGSSSLSSV TSATSSNIEQ  480
IMMQSGVNSI VPLKLHPGSN RIENGLTRDF LGMGGEGSGR AFLPQELAKF ASMGSAMGLS  540
HFNTSSH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	9e-37	182	248	3	69	Zinc finger protein JACKDAW
5b3h_F	9e-37	182	248	3	69	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	135	148	KLKQRANKDQVRKK

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00485	DAP	Transfer from AT5G03150	Download

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	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028086555.1	0.0	zinc finger protein JACKDAW
Swissprot	Q700D2	1e-127	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A2R6PWN5	0.0	A0A2R6PWN5_ACTCH; Zinc finger protein like
STRING	POPTR_0006s13130.1	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA103	24	350

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G45260.1	1e-104	C2H2-like zinc finger protein

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]