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.6KG299300.2.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: 254aa MW: 27264.7 Da PI: 10.3092

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6KG299300.2.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	20.6	1.2e-06	66	88	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y+C +Cg+ F r nL+ H r+H Pavir.6KG299300.2.p 66 YVCDICGQGFQRDQNLQMHRRRH 88 9*********************9 PP
2	zf-C2H2	12.8	0.00036	145	166	2	23
EETTTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCpdCgksFsrksnLkrHirtH 23 C C+k + +s++k H++t+ Pavir.6KG299300.2.p 145 ACARCSKAYAVHSDYKAHLKTC 166 6*******************98 PP
3	zf-C2H2	12	0.00066	174	192	5	23
TTTEEESSHHHHHHHHHHT CS zf-C2H2 5 dCgksFsrksnLkrHirtH 23 dCg++Fsr +++ H+ t+ Pavir.6KG299300.2.p 174 DCGRVFSRVESFIEHQDTC 192 9***************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.42E-6	65	88	No hit	No description
PROSITE profile	PS50157	11.572	66	88	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	8.5E-6	66	88	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0036	66	88	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	68	88	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	108	138	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.3E-4	135	165	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.42E-6	139	164	No hit	No description
SMART	SM00355	230	144	171	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: 254 aa Download sequence Send to blast
MLSSCAPTAL PPPEAGAAPP PEPPFRSLQI AATSSAKKKR RPAGTPDPDA EVVSLSPRTL 60 LESDRYVCDI CGQGFQRDQN LQMHRRRHKV PWKLLKREAG EAARKRVFVC PEPSCLHHDP 120 AHALGDLVGI KKHFRRKHSG HRQWACARCS KAYAVHSDYK AHLKTCGTRG HTCDCGRVFS 180 RVESFIEHQD TCNAGRQRAE TSSSPASGGA FGAAASTSRQ QQRRQMHATA AAAALSRTAS 240 SASPSSGGGG GDLG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-18	140	194	3	57	Zinc finger protein JACKDAW
5b3h_F	4e-18	140	194	3	57	Zinc finger protein JACKDAW
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	36	40	KKKRR
2	36	41	KKKRRP

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.28186	1e-63	root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269\|PubMed:16813575}.
Uniprot	TISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269\|PubMed:16813575}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269\|PubMed:16813575, ECO:0000269\|PubMed:18259878, ECO:0000269\|PubMed:24039602, ECO:0000269\|PubMed:9210330}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.6KG299300.2.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by auxin. {ECO:0000269\|PubMed:24039602}.

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	AK106796	0.0	AK106796.1 Oryza sativa Japonica Group cDNA clone:002-116-B04, full insert sequence.
GenBank	AK119595	0.0	AK119595.1 Oryza sativa Japonica Group cDNA clone:002-117-D09, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002444487.1	1e-136	protein indeterminate-domain 14
Swissprot	F4IPE3	1e-106	IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBL	C5YM72	1e-134	C5YM72_SORBI; Uncharacterized protein
STRING	Pavir.Fa00691.1.p	0.0	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G01940.1	1e-106	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	Pavir.6KG299300.2.p

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Kim JY,Ryu JY,Baek K,Park CM High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. New Phytol., 2016. 209(1): p. 265-79 [PMID:26256266] Ryu JY,Kim JY,Park CM Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis. Plant Signal Behav, 2015. 10(11): p. e1093715 [PMID:26452406] Qu Y, et al. Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis. J. Exp. Bot., 2017. 68(17): p. 4851-4867 [PMID:28992128] Shi H, et al. Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17. J. Pineal Res., 2018. 65(2): p. e12494 [PMID:29607541]