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.6KG032000.1.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: 160aa MW: 16765.2 Da PI: 8.9117

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6KG032000.1.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	24.4	4.8e-08	7	30	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 C+gC+ +L+Y rGA+ V+C++C t Pavir.6KG032000.1.p 7 CSGCKRVLQYRRGATGVCCPSCST 30 **********************98 PP
2	zf-LSD1	23.8	7.5e-08	46	68	1	23
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCd 23 CggC t+L Y rGA ++RC+ C Pavir.6KG032000.1.p 46 CGGCFTMLVYNRGAANIRCPHCG 68 **********************7 PP
3	zf-LSD1	25.7	1.9e-08	84	108	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GA+ V C+ C V Pavir.6KG032000.1.p 84 CGHCRTTLAYPPGASTVGCPTCRCV 108 **********************876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	2.5E-8	4	32	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.7E-6	7	30	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.4E-9	44	71	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.0E-9	46	68	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	9.4E-8	81	110	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.9E-8	84	108	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 160 aa Download sequence Send to blast
MQDQLICSGC KRVLQYRRGA TGVCCPSCST FTAANPSGSE MSELVCGGCF TMLVYNRGAA 60 NIRCPHCGRV NSTRSANQIG HLSCGHCRTT LAYPPGASTV GCPTCRCVNP VRNNNSGGSA 120 RPAPSDARPQ TVLVENPKTL DEKGKLVSNV AVGVTSWKR*

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.6KG032000.1.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004972942.1	1e-110	protein LOL4 isoform X2
Swissprot	Q84UR0	8e-77	LOL4_ORYSJ; Protein LOL4
TrEMBL	A0A368RJ30	1e-109	A0A368RJ30_SETIT; Uncharacterized protein
TrEMBL	A0A368RJH2	1e-109	A0A368RJH2_SETIT; Uncharacterized protein
STRING	Si014280m	1e-107	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP12333	29	38

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	2e-39	LSD family protein

Link Out ? help Back to Top
Phytozome	Pavir.6KG032000.1.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]