PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

evm_27.model.AmTr_v1.0_scaffold00149.55

Common Name

AMTR_s00149p00075900, LOC18437439

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

LSD

Protein Properties

Length: 144aa MW: 14916.4 Da PI: 7.7285

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00149.55	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	42.3	1.2e-13	27	51	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr+lL YP GA+sV+Ca+C++V evm_27.model.AmTr_v1.0_scaffold00149.55 27 CSGCRNLLLYPVGATSVCCAVCNAV 51 ************************9 PP
2	zf-LSD1	46.5	5.8e-15	66	90	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y rGA+sV+C++C+t+ evm_27.model.AmTr_v1.0_scaffold00149.55 66 CGGCHTLLMYIRGATSVQCSCCHTI 90 ***********************97 PP
3	zf-LSD1	40.9	3.4e-13	104	128	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C+ lL+Y +GA+sV+Ca+C++V evm_27.model.AmTr_v1.0_scaffold00149.55 104 CGNCQMLLMYQYGARSVKCAVCNFV 128 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	9.6E-13	24	54	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	2.37E-5	27	125	IPR011031	Multihaem cytochrome
Pfam	PF06943	1.4E-10	27	51	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.4E-14	63	92	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	9.5E-13	66	90	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.2E-10	101	131	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.6E-12	104	128	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: 144 aa Download sequence Send to blast
MPVPLAPYPT PPVPFTAPNG TQGQLVCSGC RNLLLYPVGA TSVCCAVCNA VTAVPPPGTE 60 MAQLICGGCH TLLMYIRGAT SVQCSCCHTI NLALEANQVA HVNCGNCQML LMYQYGARSV 120 KCAVCNFVTS VGASPSSEQK FTN*

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}.

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	3e-99	protein LSD1 isoform X1
Refseq	XP_011624573.1	3e-99	protein LSD1 isoform X1
Swissprot	Q0J7V9	2e-79	LSD1_ORYSJ; Protein LSD1
TrEMBL	W1PNK2	8e-98	W1PNK2_AMBTC; Uncharacterized protein
STRING	ERN09291	1e-98	(Amborella trichopoda)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP1146	17	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32540.3	5e-64	lsd one like 1

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00149.55
Entrez Gene	18437439

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] Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323]