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

Sopen02g009420.1

Organism

Solanum pennellii

Taxonomic ID

28526

Taxonomic Lineage

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: 196aa MW: 20867.2 Da PI: 8.285

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopen02g009420.1	genome	spenn	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	34.1	4.6e-11	17	39	1	23
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCd 23 C+gCrt+L YPrGA++V+C +C+ Sopen02g009420.1 17 CSGCRTILLYPRGATNVCCVVCN 39 **********************8 PP
2	zf-LSD1	36.5	7.8e-12	56	80	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg CrtlL+ PrGA+sVRCa+C+ V Sopen02g009420.1 56 CGCCRTLLMHPRGATSVRCACCHIV 80 9**********************98 PP
3	zf-LSD1	34.7	2.9e-11	105	128	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 Cg+ rt+L+YP GApsV+Ca+C+ Sopen02g009420.1 105 CGNSRTMLMYPCGAPSVKCAICHY 128 8888******************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	3.3E-10	15	42	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	6.6E-10	17	39	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	8.6E-14	53	83	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	6.8E-11	56	80	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.5E-11	102	132	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.5E-10	105	129	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 196 aa Download sequence Send to blast
MFENQFLVKD WYEYLVCSGC RTILLYPRGA TNVCCVVCNN LTPVPPPGME MAQLICGCCR 60 TLLMHPRGAT SVRCACCHIV NLVPVSKAYL RSTAKSPNHF AHVNCGNSRT MLMYPCGAPS 120 VKCAICHYIA HVNAVDGRTP VPVQTSNSGA TSSAGPTSST ATGHSQNQTV VVQNPMSLDE 180 SGKLVSNVVV GVTTTT

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}.

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	HG975441	2e-58	HG975441.1 Solanum pennellii chromosome ch02, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015064658.1	1e-117	protein LSD1-like
Swissprot	Q6ASS2	4e-57	LOL3_ORYSJ; Protein LOL3
TrEMBL	A0A1S4DBD8	4e-95	A0A1S4DBD8_TOBAC; protein LOL2-like
TrEMBL	A0A1U7WYC9	4e-95	A0A1U7WYC9_NICSY; protein LOL2-like isoform X1
STRING	XP_009783613.1	6e-96	(Nicotiana sylvestris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	6e-49	LSD family protein

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]