PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

LSD

Protein Properties

Length: 175aa MW: 18108 Da PI: 8.394

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400036746	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	38.3	2.2e-12	7	30	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 C+gCrt+L YPrGA++V+Ca+C++ PGSC0003DMP400036746 7 CSGCRTMLLYPRGASNVCCAVCNA 30 **********************97 PP
2	zf-LSD1	45.2	1.5e-14	46	70	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+ PrGA sVRC++C+tV PGSC0003DMP400036746 46 CGGCRTLLMHPRGANSVRCSCCHTV 70 ************************9 PP
3	zf-LSD1	39.1	1.2e-12	84	107	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 Cg+Cr +L+YP GApsV+Ca+C+ PGSC0003DMP400036746 84 CGNCRMMLMYPCGAPSVKCAVCHY 107 **********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	4.2E-13	4	32	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.4E-11	7	30	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	5.8E-17	43	73	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	7.9E-13	46	70	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	2.5E-11	81	110	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.0E-12	84	108	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 175 aa Download sequence Send to blast
MQSQLMCSGC RTMLLYPRGA SNVCCAVCNA LTPVPPPGME MAQLICGGCR TLLMHPRGAN 60 SVRCSCCHTV NLVPGPNQFA HVYCGNCRMM LMYPCGAPSV KCAVCHYITN VNAGDGRAHA 120 SLNPPNGTAT PASGSSSTAK ARSQNQTVVV QNPMSVDESG KLVSNVVVGV TTTS*

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	PGSC0003DMP400036746

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	KT036491	0.0	KT036491.1 Solanum tuberosum cultivar Kexin-4 LSD1-like protein mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006353029.1	1e-123	PREDICTED: protein LSD1
Refseq	XP_006353030.1	1e-123	PREDICTED: protein LSD1
Refseq	XP_015166652.1	1e-123	PREDICTED: protein LSD1
Swissprot	Q6ASS2	3e-66	LOL3_ORYSJ; Protein LOL3
TrEMBL	M1BWM1	1e-121	M1BWM1_SOLTU; LSD1-like protein
STRING	PGSC0003DMT400054616	1e-122	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1679	24	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32540.1	6e-55	lsd one like 1

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400036746
Entrez Gene	102606105

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] Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] Teper-Bamnolker P, et al. Release of apical dominance in potato tuber is accompanied by programmed cell death in the apical bud meristem. Plant Physiol., 2012. 158(4): p. 2053-67 [PMID:22362870]