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.3KG535400.1.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: 209aa MW: 21987.6 Da PI: 8.5521

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.3KG535400.1.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	41.6	2e-13	7	31	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr lL YPrGApsV+Ca+C++V Pavir.3KG535400.1.p 7 CHGCRSLLLYPRGAPSVCCAVCHAV 31 ************************9 PP
2	zf-LSD1	43.9	3.9e-14	75	99	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y+r+A+ VRC++CdtV Pavir.3KG535400.1.p 75 CGGCQTLLMYTRNATTVRCSCCDTV 99 ************************9 PP
3	zf-LSD1	50.5	3.3e-16	113	137	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C+t+L+YP+GApsV+Ca+C+++ Pavir.3KG535400.1.p 113 CGQCQTVLMYPYGAPSVKCAICNFI 137 ***********************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	7.0E-13	4	34	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	4.2E-11	7	31	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	6.3E-13	73	102	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.3E-11	75	99	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.2E-11	110	139	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.9E-14	113	137	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 209 aa Download sequence Send to blast
MQSQIVCHGC RSLLLYPRGA PSVCCAVCHA VTTVPPPGSA SELWFLLVHN RTSKAHALAH 60 PAHEQKGMEM ARLICGGCQT LLMYTRNATT VRCSCCDTVN LVRPVSSIAH VNCGQCQTVL 120 MYPYGAPSVK CAICNFITNI GGHQVPMVRP LPPALPASSG NSYNIPSTSA PTSQSQNVTV 180 VVENPMTVDD KGKLVSNVVV GVTTGGKK*

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.3KG535400.1.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-120	protein LOL2-like isoform X1
Swissprot	Q2QMB3	3e-93	LOL2_ORYSJ; Protein LOL2
TrEMBL	A0A2S3HFC7	1e-118	A0A2S3HFC7_9POAL; Uncharacterized protein
TrEMBL	A0A2T7EJ69	1e-118	A0A2T7EJ69_9POAL; Uncharacterized protein
STRING	Pavir.J37999.1.p	1e-151	(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	3e-41	lsd one like 1

Link Out ? help Back to Top
Phytozome	Pavir.3KG535400.1.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]