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.9NG189700.2.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

LSD

Protein Properties

Length: 136aa MW: 14159.2 Da PI: 8.6593

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.9NG189700.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	40.5	4.5e-13	6	30	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y+r A VRC++C+tV Pavir.9NG189700.2.p 6 CGGCRTLLMYTRSADTVRCSCCNTV 30 ************************9 PP
2	zf-LSD1	48.6	1.3e-15	44	68	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C+t+L+YP+GA sV+Ca+C+++ Pavir.9NG189700.2.p 44 CGHCQTTLMYPYGAHSVKCAICNHI 68 ***********************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	1.5E-15	3	33	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.3E-11	6	30	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	2.1E-11	41	69	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	9.3E-14	44	68	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 136 aa Download sequence Send to blast
MAQLICGGCR TLLMYTRSAD TVRCSCCNTV NLVRPVNNIA HVNCGHCQTT LMYPYGAHSV 60 KCAICNHITT TGVNTVAPTP SARPASNGSA YSTSSTSVPK SQPQNVTVVV ENPMTVDDKG 120 KLVSNVVVGV TTGKN*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.6444	0.0	callus\| leaf\| root

Functional Description ? help Back to Top
Source	Description
UniProt	Putative zinc finger that may be involved in programmed cell death and defense response. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.9NG189700.2.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	EU975049	1e-132	EU975049.1 Zea mays clone 466017 zinc finger protein LSD2 mRNA, complete cds.
GenBank	EU976486	1e-132	EU976486.1 Zea mays clone 895962 zinc finger protein LSD2 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025796943.1	1e-90	protein LOL3-like
Swissprot	Q6ASS2	3e-71	LOL3_ORYSJ; Protein LOL3
TrEMBL	A0A2S3IJX5	2e-90	A0A2S3IJX5_9POAL; Uncharacterized protein
TrEMBL	A0A3L6S9J3	1e-89	A0A3L6S9J3_PANMI; Uncharacterized protein
STRING	Pavir.Ia01218.1.p	4e-92	(Panicum virgatum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	1e-42	LSD family protein

Link Out ? help Back to Top
Phytozome	Pavir.9NG189700.2.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764]