PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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: 152aa MW: 15740.5 Da PI: 7.9177

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6NG062800.1.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	42.5	1.1e-13	35	59	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C gCr+lL+YP+GA+sV+Ca+C tV Pavir.6NG062800.1.p 35 CTGCRNLLMYPAGATSVCCAVCSTV 59 9**********************99 PP
2	zf-LSD1	46.7	5.2e-15	74	98	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y rGA+sV+C++C+tV Pavir.6NG062800.1.p 74 CGGCHTLLMYIRGATSVQCSCCHTV 98 ************************9 PP
3	zf-LSD1	41.8	1.8e-13	112	136	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Cr lL+Y +GA+sV+Ca+C++V Pavir.6NG062800.1.p 112 CGNCRMLLMYQYGARSVKCAVCNFV 136 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.90.10.10	2.4E-4	23	133	No hit	No description
TIGRFAMs	TIGR01053	6.7E-13	32	62	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	8.4E-11	35	59	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	3.35E-5	35	133	IPR011031	Multihaem cytochrome
TIGRFAMs	TIGR01053	9.3E-15	71	100	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.4E-12	74	98	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.2E-12	109	139	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.1E-12	112	136	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009814	Biological Process	defense response, incompatible interaction
GO:0034052	Biological Process	positive regulation of plant-type hypersensitive response
GO:2000121	Biological Process	regulation of removal of superoxide radicals

Sequence ? help Back to Top
Protein Sequence Length: 152 aa Download sequence Send to blast
MPVPLAPYPT PPVPFTPPNV SFVLQFSGAQ SQLVCTGCRN LLMYPAGATS VCCAVCSTVT 60 AVPAPGTEMA QLVCGGCHTL LMYIRGATSV QCSCCHTVNL AMEVNQVAHV NCGNCRMLLM 120 YQYGARSVKC AVCNFVTSVG ASPGAEQKPS S*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.1694	0.0	leaf\| root\| stem

Functional Description ? help Back to Top
Source	Description
UniProt	Negative regulator of programmed cell death and hypersensitive response (HR). Positive regulator of callus differentiation. {ECO:0000269\|PubMed:15915636}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.6NG062800.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By light. Down-regulated by dark. {ECO:0000269\|PubMed:15915636}.

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_006847710.1	1e-84	protein LSD1 isoform X1
Refseq	XP_011624573.1	1e-84	protein LSD1 isoform X1
Swissprot	Q0J7V9	3e-84	LSD1_ORYSJ; Protein LSD1
TrEMBL	B5KLZ6	2e-86	B5KLZ6_BAMOL; LOL1
STRING	Pavir.J40729.1.p	1e-104	(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	1e-59	lsd one like 1

Link Out ? help Back to Top
Phytozome	Pavir.6NG062800.1.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]