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.3NG284600.1.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

LSD

Protein Properties

Length: 180aa MW: 18780.9 Da PI: 8.5494

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.3NG284600.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	41.9	1.6e-13	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr lL YPrGApsV+Ca+C++V Pavir.3NG284600.1.p 7 CHGCRSLLLYPRGAPSVCCAVCHAV 31 ************************9 PP
2	zf-LSD1	44.2	3.1e-14	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y+r+A+ VRC++CdtV Pavir.3NG284600.1.p 46 CGGCQTLLMYTRNATTVRCSCCDTV 70 ************************9 PP
3	zf-LSD1	50.8	2.7e-16	84	108	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C+t+L+YP+GApsV+Ca+C+++ Pavir.3NG284600.1.p 84 CGQCQTVLMYPYGAPSVKCAICNFI 108 ***********************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	5.5E-13	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.4E-11	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	5.0E-13	44	73	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.9E-11	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	9.9E-12	81	110	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.4E-14	84	108	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 180 aa Download sequence Send to blast
MRSQIVCHGC RSLLLYPRGA PSVCCAVCHA VTTVPPPGME MARLICGGCQ TLLMYTRNAT 60 TVRCSCCDTV NLVRPVSSIA HVNCGQCQTV LMYPYGAPSV KCAICNFITN IGGHQVPTVR 120 PLPPALPASS GNSYNIPSTS APTSQSQNIT VVVENPMTVD DKGKLVSNVV VGVTTGGKK*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.7277	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.3NG284600.1.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	KF314699	0.0	KF314699.1 Setaria italica clone Si18S 18S ribosomal RNA gene, partial sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025805780.1	1e-125	protein LOL2-like isoform X1
Swissprot	Q2QMB3	7e-99	LOL2_ORYSJ; Protein LOL2
TrEMBL	A0A2S3HFC7	1e-124	A0A2S3HFC7_9POAL; Uncharacterized protein
TrEMBL	A0A2T7EJ69	1e-124	A0A2T7EJ69_9POAL; Uncharacterized protein
STRING	Pavir.J37999.1.p	1e-119	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1347	38	124

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32540.1	2e-46	lsd one like 1

Link Out ? help Back to Top
Phytozome	Pavir.3NG284600.1.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] Wu J, et al. OsLOL1, a C2C2-type zinc finger protein, interacts with OsbZIP58 to promote seed germination through the modulation of gibberellin biosynthesis in Oryza sativa. Plant J., 2014. 80(6): p. 1118-30 [PMID:25353370]