PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

C2H2

Protein Properties

Length: 535aa MW: 57532.9 Da PI: 8.8308

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.10G153200.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.1	3.3e-05	92	114	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Glyma.10G153200.1.p 92 FICEICNKGFQRDQNLQLHRRGH 114 89*******************88 PP
2	zf-C2H2	11.1	0.0012	168	190	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k + +s+ k H + + Glyma.10G153200.1.p 168 WKCDKCSKKYAVQSDWKAHSKIC 190 58*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	6.29E-7	91	114	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.4E-5	91	114	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	6.5E-5	92	114	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.845	92	114	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.022	92	114	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	94	114	IPR007087	Zinc finger, C2H2
SMART	SM00355	220	133	163	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.9E-4	156	189	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.29E-7	163	188	No hit	No description
SMART	SM00355	150	168	188	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: 535 aa Download sequence Send to blast
MSNITSCDSG SFSTENTRED AAVKQQQSEM LGQFHSPHSH TSTTTTNNSN GSNTNSQPPA 60 PVKKKRSLPG NPDPSAEVIA LSPTTLMATN RFICEICNKG FQRDQNLQLH RRGHNLPWKL 120 KQRTSTEIRK RVYVCPEPSC VHHNPARALG DLTGIKKHFC RKHGEKKWKC DKCSKKYAVQ 180 SDWKAHSKIC GTREYKCDCG TIFSRRDSFI THRAFCDALA EENNKANEGQ LPKIGPNLQC 240 QQIPNLVSSL PINTNSIVPN PAQMGGTTSE FNHADHKHPL SLPHELMPMP AQKPFNNNMA 300 AGTVFTRSLS STSSPSLQLS SNMFDENGLH LAAGSPHMSA TALLQKAAQM GATLTEKSTF 360 ATNMAPPSFG VLQQHHHHQQ PNGQPFTNQY MHSGHHHQQQ EVNISTQYSF GSANGMGGGS 420 VGMNGVDMFN AILDQSKALS KIIEQNNNRS SSGGTTNGGS SSAINNVAGS KGSGDVMTLD 480 FLGIGGGGSG SGGGAHGNFY GGAQQGETGA PDEVWRNWSS KNAGFESFST TSSI*

Sequence ? help Back to Top

Protein Sequence Length: 535 aa Download sequence Send to blast

MSNITSCDSG SFSTENTRED AAVKQQQSEM LGQFHSPHSH TSTTTTNNSN GSNTNSQPPA  60
PVKKKRSLPG NPDPSAEVIA LSPTTLMATN RFICEICNKG FQRDQNLQLH RRGHNLPWKL  120
KQRTSTEIRK RVYVCPEPSC VHHNPARALG DLTGIKKHFC RKHGEKKWKC DKCSKKYAVQ  180
SDWKAHSKIC GTREYKCDCG TIFSRRDSFI THRAFCDALA EENNKANEGQ LPKIGPNLQC  240
QQIPNLVSSL PINTNSIVPN PAQMGGTTSE FNHADHKHPL SLPHELMPMP AQKPFNNNMA  300
AGTVFTRSLS STSSPSLQLS SNMFDENGLH LAAGSPHMSA TALLQKAAQM GATLTEKSTF  360
ATNMAPPSFG VLQQHHHHQQ PNGQPFTNQY MHSGHHHQQQ EVNISTQYSF GSANGMGGGS  420
VGMNGVDMFN AILDQSKALS KIIEQNNNRS SSGGTTNGGS SSAINNVAGS KGSGDVMTLD  480
FLGIGGGGSG SGGGAHGNFY GGAQQGETGA PDEVWRNWSS KNAGFESFST TSSI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-33	164	222	3	61	Zinc finger protein JACKDAW
5b3h_F	1e-33	164	222	3	61	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.33088	0.0	cotyledon\| leaf\| root\| stem

Expression -- Description ? help Back to Top
Source	Description
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: Observed in vegetative tissues. Mainly expressed in hypocotyls, petioles, shoot apices, root tips, and trichomes, and, at low levels, in leaves, stems and flowers. {ECO:0000269\|PubMed:25035403}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling. GA converts the GAF1 complex from transcriptional activator to repressor via the degradation of DELLA proteins. {ECO:0000269\|PubMed:25035403}.
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.10G153200.1.p

Regulation -- Description ? help Back to Top
Source	Description
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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC235914	0.0	AC235914.2 Glycine max clone GM_WBc0225O17, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003535336.1	0.0	protein indeterminate-domain 2
Refseq	XP_028184221.1	0.0	zinc finger protein GAI-ASSOCIATED FACTOR 1-like
Swissprot	Q9SCQ6	1e-114	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
Swissprot	Q9ZWA6	1e-114	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	A0A445IMU1	0.0	A0A445IMU1_GLYSO; Protein indeterminate-domain 2
TrEMBL	I1LBB3	0.0	I1LBB3_SOYBN; Uncharacterized protein
STRING	GLYMA10G29390.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2192	30	85
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-101	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Glyma.10G153200.1.p
Entrez Gene	100813556

Publications ? help Back to Top
Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] 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] Khare D, et al. Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana. New Phytol., 2017. 213(3): p. 1257-1273 [PMID:27768815]