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

Pavir.5NG619300.1.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 524aa MW: 55228.3 Da PI: 8.2706

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.5NG619300.1.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	103	125	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Pavir.5NG619300.1.p 103 FVCEICHKGFQRDQNLQLHRRGH 125 89*******************88 PP
2	zf-C2H2	12.3	0.00051	215	233	5	23
TTTEEESSHHHHHHHHHHT CS zf-C2H2 5 dCgksFsrksnLkrHirtH 23 dCg++Fsr++++++H + Pavir.5NG619300.1.p 215 DCGTVFSRRDSFVTHRAFC 233 9**************8765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.44E-5	102	125	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.9E-5	102	125	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.637	103	125	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	105	125	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.0E-4	173	205	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.44E-5	180	205	No hit	No description

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: 524 aa Download sequence Send to blast
MSGAAARECA GSFSSVSSNN TASREVEEEF LHHQQRQFHI KPLLGSPPEM GTDDGDLQRV 60 TGPSEPPPAL PTVKKKRSLP GTPDPSAEVI ALSPRTLMAT NRFVCEICHK GFQRDQNLQL 120 HRRGHNLPWK LRQRGGGADA AGGPPRKRVY VCPKASCVHH NPARALGDLT GIKKHYCRKH 180 GEKKWKCERC AKRYAVHSDW KAHAKVCGTR EYKCDCGTVF SRRDSFVTHR AFCDALAEEN 240 NKLAQPMNMA TVASALQGQA AHHLAFPPSH SHLQEADAAE DDAADDFALD TKSPQLRMLP 300 PAMSDDAAAP LLPPLSMAGC MLSSLAAARP APSPSAAFFT GARIGLDGPS DPSRSMGGGF 360 SATASMSATA LLQKAAEMGA TTGGGGYGYG AGFATVGFGP MLGGPDRLPA MSPFGPLKAD 420 PPPYDGLPLG HAQLVGLDAG RLLPGQLYYG GSNGGAVGSM MHGAYGSSAA DDGSLMHGGQ 480 QQQTTEHRRP DGLRVVDYLG VDDQRTFSGS GVSPFGPHLG PWA*

Sequence ? help Back to Top

Protein Sequence Length: 524 aa Download sequence Send to blast

MSGAAARECA GSFSSVSSNN TASREVEEEF LHHQQRQFHI KPLLGSPPEM GTDDGDLQRV  60
TGPSEPPPAL PTVKKKRSLP GTPDPSAEVI ALSPRTLMAT NRFVCEICHK GFQRDQNLQL  120
HRRGHNLPWK LRQRGGGADA AGGPPRKRVY VCPKASCVHH NPARALGDLT GIKKHYCRKH  180
GEKKWKCERC AKRYAVHSDW KAHAKVCGTR EYKCDCGTVF SRRDSFVTHR AFCDALAEEN  240
NKLAQPMNMA TVASALQGQA AHHLAFPPSH SHLQEADAAE DDAADDFALD TKSPQLRMLP  300
PAMSDDAAAP LLPPLSMAGC MLSSLAAARP APSPSAAFFT GARIGLDGPS DPSRSMGGGF  360
SATASMSATA LLQKAAEMGA TTGGGGYGYG AGFATVGFGP MLGGPDRLPA MSPFGPLKAD  420
PPPYDGLPLG HAQLVGLDAG RLLPGQLYYG GSNGGAVGSM MHGAYGSSAA DDGSLMHGGQ  480
QQQTTEHRRP DGLRVVDYLG VDDQRTFSGS GVSPFGPHLG PWA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-33	181	248	3	70	Zinc finger protein JACKDAW
5b3h_F	1e-33	181	248	3	70	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.5NG619300.1.p

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	BT066652	0.0	BT066652.1 Zea mays full-length cDNA clone ZM_BFb0043G06 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025817951.1	0.0	protein indeterminate-domain 2-like
Swissprot	Q9SCQ6	1e-106	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	A0A2T7DBX2	0.0	A0A2T7DBX2_9POAL; Uncharacterized protein
STRING	Si001316m	0.0	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP12554	25	34

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-102	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Pavir.5NG619300.1.p

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] 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]