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

PSME_00053892-RA

Organism

Pseudotsuga menziesii

Taxonomic ID

3357

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga

Family

LSD

Protein Properties

Length: 130aa MW: 13728.2 Da PI: 7.5255

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PSME_00053892-RA	genome	PRS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	37.4	4.3e-12	26	50	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCrtlL YP GAp+V+Ca+C tV PSME_00053892-RA 26 CSGCRTLLVYPQGAPNVCCAVCITV 50 **********************998 PP
2	zf-LSD1	37.8	3.2e-12	64	88	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+CrtlL+Y GA+sV+C++C tV PSME_00053892-RA 64 CGHCRTLLMYAHGATSVQCSCCSTV 88 ***********************99 PP
3	zf-LSD1	40.1	6e-13	102	126	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C t+L+YP+G ps++CalC++V PSME_00053892-RA 102 CGNCFTTLMYPYGDPSIKCALCHFV 126 ***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	3.2E-12	23	53	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.5E-11	26	50	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.4E-13	61	90	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	3.1E-11	64	88	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.9E-10	99	129	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.9E-11	102	126	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 130 aa Download sequence Send to blast
MPLHMNPFPP QPMPLPPLNG KGQLVCSGCR TLLVYPQGAP NVCCAVCITV TAVPPGAEMA 60 QLICGHCRTL LMYAHGATSV QCSCCSTVNL AMEANQVAHV NCGNCFTTLM YPYGDPSIKC 120 ALCHFVTNVG

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT071760	1e-116	BT071760.1 Picea sitchensis clone WS0452_N14 unknown mRNA.
GenBank	EF084706	1e-116	EF084706.1 Picea sitchensis clone WS02727_J11 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006847710.1	2e-54	protein LSD1 isoform X1
Refseq	XP_010269986.1	1e-54	PREDICTED: protein LSD1
Refseq	XP_010269987.1	1e-54	PREDICTED: protein LSD1
Refseq	XP_010269988.1	1e-54	PREDICTED: protein LSD1
Refseq	XP_010941225.1	1e-54	protein LSD1 isoform X2
Refseq	XP_010941226.1	1e-54	protein LSD1 isoform X2
Refseq	XP_011624573.1	2e-54	protein LSD1 isoform X1
Swissprot	Q0J7V9	6e-53	LSD1_ORYSJ; Protein LSD1
TrEMBL	A0A0C9RP33	1e-66	A0A0C9RP33_9SPER; TSA: Wollemia nobilis Ref_Wollemi_Transcript_6820_1247 transcribed RNA sequence
STRING	ERN09291	6e-54	(Amborella trichopoda)
STRING	XP_010269986.1	5e-54	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32540.1	4e-46	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]