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

Sevir.9G247100.1.p

Organism

Setaria viridis

Taxonomic ID

4556

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria

Family

C2H2

Protein Properties

Length: 456aa MW: 48956.4 Da PI: 8.5844

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sevir.9G247100.1.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	17.4	1.3e-05	83	105	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Sevir.9G247100.1.p 83 FVCEICNKGFQRDQNLQLHRRGH 105 89*******************88 PP
2	zf-C2H2	13.8	0.00018	172	194	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C+ Cgk++ +s+ k H + + Sevir.9G247100.1.p 172 WRCERCGKRYAVQSDWKAHVKGC 194 58*****************9866 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.5E-5	82	105	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.95E-9	82	105	No hit	No description
SMART	SM00355	0.017	83	105	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	7.1E-5	83	105	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.949	83	105	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	85	105	IPR007087	Zinc finger, C2H2
SMART	SM00355	89	137	167	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.0E-4	160	192	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.95E-9	167	192	No hit	No description
SMART	SM00355	95	172	192	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: 456 aa Download sequence Send to blast
MMLSDLSSDH EATGSSSHGG DIASYALSPL FLAPAPPLAG AAAPQTEAPR VGAKRKRSQP 60 GNPDPGAEVI ALSPRTLVAT NRFVCEICNK GFQRDQNLQL HRRGHNLPWK LRQRSLPSGA 120 GGRQGDAAAA PPRKRVYVCP EPTCVHHDPA RALGDLTGIK KHFSRKHGEK RWRCERCGKR 180 YAVQSDWKAH VKGCGTREYR CDCGILFTRL IDQLGTYVLA PTKNRSYAAL LDFICSCWVE 240 YQCMKDSLLT HRAFCDALAE ESARILAAAN NGSTITTTNS SNGGNSGSDL LFSNSSGVVT 300 PLFLPFPNPP PSPPPPAAAA AQNPNAFYFL HHQEQQLAAP FLHPRMVQPS PYLDLHADAA 360 AVTTATCGGI GADTVNFGLA PDGSVALRHR RLTRDFLGVD GGSQVEELQL PIYATAAAAA 420 ATVVPRAASC ATDLTRQYLG ERPLPPVNET WSHNF*

Sequence ? help Back to Top

Protein Sequence Length: 456 aa Download sequence Send to blast

MMLSDLSSDH EATGSSSHGG DIASYALSPL FLAPAPPLAG AAAPQTEAPR VGAKRKRSQP  60
GNPDPGAEVI ALSPRTLVAT NRFVCEICNK GFQRDQNLQL HRRGHNLPWK LRQRSLPSGA  120
GGRQGDAAAA PPRKRVYVCP EPTCVHHDPA RALGDLTGIK KHFSRKHGEK RWRCERCGKR  180
YAVQSDWKAH VKGCGTREYR CDCGILFTRL IDQLGTYVLA PTKNRSYAAL LDFICSCWVE  240
YQCMKDSLLT HRAFCDALAE ESARILAAAN NGSTITTTNS SNGGNSGSDL LFSNSSGVVT  300
PLFLPFPNPP PSPPPPAAAA AQNPNAFYFL HHQEQQLAAP FLHPRMVQPS PYLDLHADAA  360
AVTTATCGGI GADTVNFGLA PDGSVALRHR RLTRDFLGVD GGSQVEELQL PIYATAAAAA  420
ATVVPRAASC ATDLTRQYLG ERPLPPVNET WSHNF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	7e-27	168	271	3	71	Zinc finger protein JACKDAW
5b3h_F	7e-27	168	271	3	71	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that acts as a flowering master switch in both long and short days, independently of the circadian clock (PubMed:18790997, PubMed:18725639, PubMed:18774969, PubMed:19304997, PubMed:24280027). Promotes flowering upstream of HD1 by up-regulating FTL1, FTL4, FTL5, FTL6, EHD1, HD3A and RFT1 (PubMed:18790997, PubMed:18725639, PubMed:18774969). Seems to repress FTL11 expression (PubMed:18725639). May recognize the consensus motif 5'-TTTGTCGTAAT-3' in target gene promoters (PubMed:18725639). {ECO:0000269\|PubMed:18725639, ECO:0000269\|PubMed:18774969, ECO:0000269\|PubMed:18790997, ECO:0000269\|PubMed:24280027, ECO:0000303\|PubMed:19304997}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00673	SELEX	Transfer from GRMZM2G011357	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sevir.9G247100.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by FKF1 (PubMed:25850808). Down-regulated by DLF1 (PubMed:25036785). During the basic vegetative growth phase (BVP, photoperiod-insensitive phase), suppressed via phytochrome-mediated light signals involving the phytochromobilin synthase HY2 (PubMed:25573482). {ECO:0000269\|PubMed:25036785, ECO:0000269\|PubMed:25573482, ECO:0000269\|PubMed:25850808}.

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_004983079.1	0.0	protein indeterminate-domain 12
Swissprot	B1B534	1e-132	EHD2_ORYSJ; Protein EARLY HEADING DATE 2
TrEMBL	A0A368SKG6	0.0	A0A368SKG6_SETIT; Uncharacterized protein
STRING	Si036003m	0.0	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP13096	28	32

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G55110.1	1e-91	indeterminate(ID)-domain 7

Link Out ? help Back to Top
Phytozome	Sevir.9G247100.1.p

Publications ? help Back to Top
Rice Chromosome 10 Sequencing Consortium In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 2003. 300(5625): p. 1566-9 [PMID:12791992] Park SJ, et al. Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod. Plant J., 2008. 56(6): p. 1018-29 [PMID:18774969] Song Y,Gao Z,Luan W Interaction between temperature and photoperiod in regulation of flowering time in rice. Sci China Life Sci, 2012. 55(3): p. 241-9 [PMID:22527521] Hu S, et al. A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7. Rice (N Y), 2013. 6(1): p. 24 [PMID:24280027] Cai Y, et al. Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice. PLoS ONE, 2014. 9(7): p. e102529 [PMID:25036785] Yoshitake Y, et al. The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice. Sci Rep, 2015. 5: p. 7709 [PMID:25573482] Han SH,Yoo SC,Lee BD,An G,Paek NC Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod. Plant Cell Environ., 2015. 38(12): p. 2527-40 [PMID:25850808] Jin J, et al. MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice. Plant Physiol., 2015. 168(4): p. 1275-85 [PMID:25855537] Brambilla V,Gomez-Ariza J,Cerise M,Fornara F The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals. Front Plant Sci, 2017. 8: p. 665 [PMID:28491078]