PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

C2H2

Protein Properties

Length: 478aa MW: 52064.5 Da PI: 8.8464

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.007G135000.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.7	4.3e-05	64	84	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H Potri.007G135000.1 64 CEICGKGFQRDQNLQLHRRGH 84 *******************88 PP
2	zf-C2H2	13.5	0.00022	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Potri.007G135000.1 138 WKCEKCSKRYAVQSDWKAHSKTC 160 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.58E-6	61	84	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.1E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.489	62	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.076	62	84	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.6E-4	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.58E-6	133	158	No hit	No description
SMART	SM00355	130	138	158	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010150	Biological Process	leaf senescence
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0048573	Biological Process	photoperiodism, flowering
GO:0005634	Cellular Component	nucleus
GO:0044212	Molecular Function	transcription regulatory region DNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 478 aa Download sequence Send to blast
MSENIMAAEE AITSSYNGSV ENPVGGSNPP ALKKKRNLPG TPDPEAEVIA LSPKTLMATN 60 RFLCEICGKG FQRDQNLQLH RRGHNLPWKL KQRTNNEVRK RVYVCPEKTC VHHHPSRALG 120 DLTGIKKHFC RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYKCDCG TLFSRRDSFI 180 THRAFCDALA EETARVNAVS SIRNLTAGNI SYHLPGNPLG PNMAQHFSSI FKPISSNDHH 240 TRQGGLSLWM HQGGVPHVSE AMGNNIQEIH QIGAMTSSGA IFGDPLAVSC SSTPPSDHYQ 300 LNWPVFGNKI SSNNAHEELT STLVLPLSNV KEAAAASQLV SVPSLYSTQQ QQSHQTTSAN 360 MSATALLQKA TQIGATSTDP SFLGSFGLKS FSTKAQDGNN KFCGLYGSSP ISTNPASDME 420 NSGNDEIPTL NQLQMYSAKR QKIFQSDQDS PAGGQTRDFL GVGVQAICHP SSINGWI*

Sequence ? help Back to Top

Protein Sequence Length: 478 aa Download sequence Send to blast

MSENIMAAEE AITSSYNGSV ENPVGGSNPP ALKKKRNLPG TPDPEAEVIA LSPKTLMATN  60
RFLCEICGKG FQRDQNLQLH RRGHNLPWKL KQRTNNEVRK RVYVCPEKTC VHHHPSRALG  120
DLTGIKKHFC RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYKCDCG TLFSRRDSFI  180
THRAFCDALA EETARVNAVS SIRNLTAGNI SYHLPGNPLG PNMAQHFSSI FKPISSNDHH  240
TRQGGLSLWM HQGGVPHVSE AMGNNIQEIH QIGAMTSSGA IFGDPLAVSC SSTPPSDHYQ  300
LNWPVFGNKI SSNNAHEELT STLVLPLSNV KEAAAASQLV SVPSLYSTQQ QQSHQTTSAN  360
MSATALLQKA TQIGATSTDP SFLGSFGLKS FSTKAQDGNN KFCGLYGSSP ISTNPASDME  420
NSGNDEIPTL NQLQMYSAKR QKIFQSDQDS PAGGQTRDFL GVGVQAICHP SSINGWI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	9e-37	134	200	3	69	Zinc finger protein JACKDAW
5b3h_F	9e-37	134	200	3	69	Zinc finger protein JACKDAW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed throughout development. {ECO:0000269\|PubMed:21265895}.
Uniprot	TISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:25829440}.
Uniprot	TISSUE SPECIFICITY: Highly expressed in vegetative organs and at lower levels in flowers and siliques. Expressed predominantly in roots. In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269\|PubMed:21265895, ECO:0000269\|PubMed:25829440, ECO:0000305\|PubMed:21265895}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds to the DNA sequence 5'-CTTTTGTCC-3' (PubMed:21265895, PubMed:25929516). Regulates photoperiodic flowering by modulating sugar transport and metabolism (PubMed:21265895, PubMed:25929516). Regulates SUS1 and SUS4 (PubMed:21265895). Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:25829440). {ECO:0000269\|PubMed:21265895, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:25929516}.
UniProt	Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). 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). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00125	DAP	Transfer from AT1G03840	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Potri.007G135000.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by 'SHORT-ROOT' (SHR)(PubMed:16640459). Strongly down-regulated by sugar deprivation, but not regulated by day-length. {ECO:0000269\|PubMed:16640459}.
UniProt	INDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {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_006380280.1	0.0	zinc finger protein NUTCRACKER
Swissprot	Q9FFH3	1e-154	IDD8_ARATH; Zinc finger protein NUTCRACKER
Swissprot	Q9ZWA6	1e-154	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	U5G9H1	0.0	U5G9H1_POPTR; Uncharacterized protein
STRING	POPTR_0007s01380.1	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4626	29	51
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-150	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Potri.007G135000.1
Entrez Gene	18100839

Publications ? help Back to Top
Muñoz-Strale D,León G Identification of two highly specific pollen promoters using transcriptomic data. Plant Physiol. Biochem., 2014. 83: p. 292-9 [PMID:25208507] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] 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]