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

ORGLA08G0030200.1

Organism

Oryza glaberrima

Taxonomic ID

4538

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

LSD

Protein Properties

Length: 201aa MW: 21010.6 Da PI: 7.9543

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
ORGLA08G0030200.1	genome	AGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	43.4	5.4e-14	85	109	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr+lL+YP+GA+sV+Ca+C tV ORGLA08G0030200.1 85 CSGCRNLLMYPAGATSVCCAVCSTV 109 ***********************99 PP
2	zf-LSD1	46.1	7.8e-15	124	148	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y rGA+sV+C++C+tV ORGLA08G0030200.1 124 CGGCHTLLMYIRGATSVQCSCCHTV 148 ************************9 PP
3	zf-LSD1	41.2	2.7e-13	162	186	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Cr lL+Y +GA+sV+Ca+C++V ORGLA08G0030200.1 162 CGNCRMLLMYQYGARSVKCAVCNFV 186 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	1.7E-13	82	112	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	1.95E-5	85	183	IPR011031	Multihaem cytochrome
Pfam	PF06943	2.9E-11	85	109	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.5E-14	121	150	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.1E-12	124	148	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	6.6E-12	159	189	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.7E-12	162	186	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:0034051	Biological Process	negative regulation of plant-type hypersensitive response
GO:0034052	Biological Process	positive regulation of plant-type hypersensitive response
GO:0045595	Biological Process	regulation of cell differentiation
GO:2000121	Biological Process	regulation of removal of superoxide radicals

Sequence ? help Back to Top
Protein Sequence Length: 201 aa Download sequence Send to blast
MCIAEPIFCC IKSPETSCCK LKRFLSCRER KGDFSCLTAA RICEASTSDA VVQAAGTAMP 60 VPLAPYPTPP VPFTPPNGAQ SQLVCSGCRN LLMYPAGATS VCCAVCSTVT AVPAPGTEMA 120 QLVCGGCHTL LMYIRGATSV QCSCCHTVNL AMEANQVAHV NCGNCRMLLM YQYGARSVKC 180 AVCNFVTSVG ASPGTDQKPS S

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	ORGLA08G0030200.1

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	AK111759	0.0	AK111759.1 Oryza sativa Japonica Group cDNA clone:J023055E16, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015648106.1	1e-144	protein LSD1 isoform X3
Refseq	XP_015648107.1	1e-144	protein LSD1 isoform X3
Swissprot	Q0J7V9	1e-127	LSD1_ORYSJ; Protein LSD1
TrEMBL	I1QFV1	1e-143	I1QFV1_ORYGL; Uncharacterized protein
STRING	ORGLA08G0030200.1	1e-143	(Oryza glaberrima)

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	3e-60	lsd one like 1

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]