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: 144aa MW: 14804.3 Da PI: 7.9177

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6KG062100.1.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	42.6	9.9e-14	27	51	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C gCr+lL+YP+GA+sV+Ca+C tV Pavir.6KG062100.1.p 27 CTGCRNLLMYPAGATSVCCAVCSTV 51 9**********************99 PP
2	zf-LSD1	46.8	4.8e-15	66	90	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y rGA+sV+C++C+tV Pavir.6KG062100.1.p 66 CGGCHTLLMYIRGATSVQCSCCHTV 90 ************************9 PP
3	zf-LSD1	41.9	1.7e-13	104	128	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Cr lL+Y +GA+sV+Ca+C++V Pavir.6KG062100.1.p 104 CGNCRMLLMYQYGARSVKCAVCNFV 128 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.90.10.10	9.5E-4	22	125	No hit	No description
TIGRFAMs	TIGR01053	6.1E-13	24	54	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	5.86E-5	27	125	IPR011031	Multihaem cytochrome
Pfam	PF06943	7.7E-11	27	51	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	8.5E-15	63	92	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.3E-12	66	90	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	3.9E-12	101	131	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.0E-12	104	128	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0034051	Biological Process	negative regulation of plant-type hypersensitive response
GO:0045595	Biological Process	regulation of cell differentiation

Sequence ? help Back to Top
Protein Sequence Length: 144 aa Download sequence Send to blast
MPVPLAPYPT PPVPFTPPNG AQSQLVCTGC RNLLMYPAGA TSVCCAVCST VTAVPAPGTE 60 MAQLVCGGCH TLLMYIRGAT SVQCSCCHTV NLAMEANQVA HVNCGNCRML LMYQYGARSV 120 KCAVCNFVTS VGASPGAEQK PSS*

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.6KG062100.1.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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	FP091666	1e-153	FP091666.1 Phyllostachys edulis cDNA clone: bphyst007l18, full insert sequence.
GenBank	FP094210	1e-153	FP094210.1 Phyllostachys edulis cDNA clone: bphylf003c20, full insert sequence.
GenBank	FP097106	1e-153	FP097106.1 Phyllostachys edulis cDNA clone: bphyst016n22, full insert sequence.
GenBank	FP097837	1e-153	FP097837.1 Phyllostachys edulis cDNA clone: bphylf033i22, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002445097.1	9e-99	protein LSD1
Refseq	XP_004972784.2	9e-99	protein LSD1
Refseq	XP_022683193.1	9e-99	protein LSD1
Refseq	XP_025820445.1	9e-99	protein LSD1
Refseq	XP_025820446.1	9e-99	protein LSD1
Refseq	XP_025820447.1	9e-99	protein LSD1
Refseq	XP_025820449.1	9e-99	protein LSD1
Swissprot	Q0J7V9	1e-87	LSD1_ORYSJ; Protein LSD1
TrEMBL	A0A2T7D3S8	2e-97	A0A2T7D3S8_9POAL; Uncharacterized protein
TrEMBL	A0A2T8IF35	2e-97	A0A2T8IF35_9POAL; Uncharacterized protein
TrEMBL	C5YHD0	2e-97	C5YHD0_SORBI; Uncharacterized protein
TrEMBL	K3YK34	2e-97	K3YK34_SETIT; Uncharacterized protein
STRING	Pavir.Fa01884.1.p	4e-98	(Panicum virgatum)
STRING	Si014603m	4e-98	(Setaria italica)
STRING	Sb07g004050.1	4e-98	(Sorghum bicolor)

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
AT1G32540.3	1e-59	lsd one like 1

Link Out ? help Back to Top
Phytozome	Pavir.6KG062100.1.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]