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; Lycopersicon

Family

LSD

Protein Properties

Length: 379aa MW: 41308.9 Da PI: 4.334

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc02g078270.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	36.4	8.6e-12	289	313	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+ lLsY GA++V+C++C+tV Solyc02g078270.2.1 289 CGGCQQLLSYSQGAKLVKCSCCQTV 313 ************************9 PP
2	zf-LSD1	44.5	2.6e-14	327	351	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC +lL+YP+GApsVRC++C ++ Solyc02g078270.2.1 327 CGGCAVLLMYPYGAPSVRCSSCRHM 351 **********************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	5.9E-14	286	316	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.3E-9	289	313	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	6.3E-10	324	352	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	8.3E-12	327	350	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009617	Biological Process	response to bacterium

Sequence ? help Back to Top
Protein Sequence Length: 379 aa Download sequence Send to blast
MEEKLSHIEN QQLDDDEEED EGPPPGFDSL AVPSQNTNVV IDEDDDEGPP PGWPSIPQQH 60 NLQTTDVEMG SKEHKSEDDE DGPPPGWNTV ISQKKSPSSP PTLEAVICDI EMEKKEEIIK 120 NEDNGPPPIW QLTPKLPALQ TSTPPSWTQG ASLEDIEMEK KEEAVEDEDN GPPPGWQLTP 180 QLLPLQTSTP PSGIQGAPLA DVEMASNQDC DVEKEGHPLG SPTPPLQSSS PVASSEMDMG 240 RKQEGTKNEE ERPPSEKQPM SHLVQMKPIV PQASSHAATV SSELGQMVCG GCQQLLSYSQ 300 GAKLVKCSCC QTVNLVLEAH EVGQVKCGGC AVLLMYPYGA PSVRCSSCRH MTKIWAHNRR 360 PPQSVQQPRR RHPSYQVH*

Sequence ? help Back to Top

Protein Sequence Length: 379 aa Download sequence Send to blast

MEEKLSHIEN QQLDDDEEED EGPPPGFDSL AVPSQNTNVV IDEDDDEGPP PGWPSIPQQH  60
NLQTTDVEMG SKEHKSEDDE DGPPPGWNTV ISQKKSPSSP PTLEAVICDI EMEKKEEIIK  120
NEDNGPPPIW QLTPKLPALQ TSTPPSWTQG ASLEDIEMEK KEEAVEDEDN GPPPGWQLTP  180
QLLPLQTSTP PSGIQGAPLA DVEMASNQDC DVEKEGHPLG SPTPPLQSSS PVASSEMDMG  240
RKQEGTKNEE ERPPSEKQPM SHLVQMKPIV PQASSHAATV SSELGQMVCG GCQQLLSYSQ  300
GAKLVKCSCC QTVNLVLEAH EVGQVKCGGC AVLLMYPYGA PSVRCSSCRH MTKIWAHNRR  360
PPQSVQQPRR RHPSYQVH*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.12703	3e-75	fruit

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	9433316	3e-75

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc02g078270.2.1

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	AC226513	1e-102	Solanum lycopersicum chromosome 2 clone C02SLe0005F12, complete sequence

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004232872.1	0.0	uncharacterized protein LOC101248737 isoform X2
TrEMBL	A0A3Q7F3X0	0.0	A0A3Q7F3X0_SOLLC; Uncharacterized protein
STRING	Solyc02g078270.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA11642	22	23
Representative plant	OGRP1146	17	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G21610.1	3e-30	lsd one like 2

Link Out ? help Back to Top
Phytozome	Solyc02g078270.2.1
Entrez Gene	101248737

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505]