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: 550aa MW: 60179.9 Da PI: 9.5152

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.20G005800.1.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	16.3	2.8e-05	79	101	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Glyma.20G005800.1.p 79 FICEVCNKGFQREQNLQLHRRGH 101 89*******************88 PP
2	zf-C2H2	12.6	0.00041	155	177	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Glyma.20G005800.1.p 155 WKCEKCSKKYAVQSDWKAHSKTC 177 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	6.1E-6	78	101	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.18E-7	78	101	No hit	No description
Pfam	PF12171	2.7E-5	79	101	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.99	79	101	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0052	79	101	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	81	101	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	120	150	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.2E-5	143	176	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.18E-7	150	175	No hit	No description
SMART	SM00355	140	155	175	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: 550 aa Download sequence Send to blast
MASASSSTPF LGIRQENQSH VTQQQQHQSS TTAASSTTTT SATPTTVPQK KRRNQPGTPY 60 PDAEVIALSP KTLMATNRFI CEVCNKGFQR EQNLQLHRRG HNLPWKLKQK TNKEPKRKVY 120 LCPEPTCVHH DPSRALGDLT GIKKHYSRKH GEKKWKCEKC SKKYAVQSDW KAHSKTCGTR 180 EYRCDCGTLF SRRDSFITHR AFCDALAHDS ARHPSSLNPL GTHHLYGTNH MSLGLSAQLQ 240 NHQAATNSIL SLGSAPKFEH LISPNLHHSP SSFGVQSPPP PPQSSSFFMT DPNQAFQDLQ 300 SQNQGHLFSN KQLHGLMQLP DLQGTTNINS TTSASSVSGS ANNTNLFNLS FFPNTNASGS 360 IINDQFSNMT GVTNNNQGTA TLYSTNSPVN SNQVGLSSLF GNSSVQQDNM SPHMSATALL 420 QKAAQMGSTT TTNELGMRSS MEDDEHSNHL RGLMNSFVNG NNLGQFHNVV EEPKKMPQNN 480 NLGLCFGGSD KLTLDFLGVG GMVRNMNNGG GFSQREQQQQ QHSMGITMSP LDPKLESAKA 540 NQHYGTSTL*

Sequence ? help Back to Top

Protein Sequence Length: 550 aa Download sequence Send to blast

MASASSSTPF LGIRQENQSH VTQQQQHQSS TTAASSTTTT SATPTTVPQK KRRNQPGTPY  60
PDAEVIALSP KTLMATNRFI CEVCNKGFQR EQNLQLHRRG HNLPWKLKQK TNKEPKRKVY  120
LCPEPTCVHH DPSRALGDLT GIKKHYSRKH GEKKWKCEKC SKKYAVQSDW KAHSKTCGTR  180
EYRCDCGTLF SRRDSFITHR AFCDALAHDS ARHPSSLNPL GTHHLYGTNH MSLGLSAQLQ  240
NHQAATNSIL SLGSAPKFEH LISPNLHHSP SSFGVQSPPP PPQSSSFFMT DPNQAFQDLQ  300
SQNQGHLFSN KQLHGLMQLP DLQGTTNINS TTSASSVSGS ANNTNLFNLS FFPNTNASGS  360
IINDQFSNMT GVTNNNQGTA TLYSTNSPVN SNQVGLSSLF GNSSVQQDNM SPHMSATALL  420
QKAAQMGSTT TTNELGMRSS MEDDEHSNHL RGLMNSFVNG NNLGQFHNVV EEPKKMPQNN  480
NLGLCFGGSD KLTLDFLGVG GMVRNMNNGG GFSQREQQQQ QHSMGITMSP LDPKLESAKA  540
NQHYGTSTL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-34	151	218	3	70	Zinc finger protein JACKDAW
5b3h_F	1e-34	151	218	3	70	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.13449	0.0	cotyledon\| leaf\| pod

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305\|PubMed:22898356}.

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}.
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). 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:24821766, ECO:0000305\|PubMed:19726569}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.20G005800.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

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	AC160454	1e-165	AC160454.31 Glycine max cultivar Williams 82 clone gmw1-15k6, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006605451.1	0.0	protein indeterminate-domain 5, chloroplastic
Refseq	XP_006605452.1	0.0	protein indeterminate-domain 5, chloroplastic
Refseq	XP_028222360.1	0.0	protein indeterminate-domain 5, chloroplastic-like
Refseq	XP_028222361.1	0.0	protein indeterminate-domain 5, chloroplastic-like
Swissprot	Q8GYC1	1e-133	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
Swissprot	Q9ZUL3	1e-132	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A0B2NUV5	0.0	A0A0B2NUV5_GLYSO; Protein indeterminate-domain 4, chloroplastic isoform B
TrEMBL	I1NCZ9	0.0	I1NCZ9_SOYBN; Uncharacterized protein
STRING	GLYMA20G00840.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1536	33	97
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	1e-109	indeterminate(ID)-domain 4

Link Out ? help Back to Top
Phytozome	Glyma.20G005800.1.p
Entrez Gene	102663407

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]