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

Cc06_g12860

Common Name

GSCOC_T00041482001

Organism

Coffea canephora

Taxonomic ID

49390

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea

Family

LSD

Protein Properties

Length: 181aa MW: 18998.2 Da PI: 8.5504

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cc06_g12860	genome	CGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	36.7	6.9e-12	7	30	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 C+gCr +L YPrGA++V+Ca C++ Cc06_g12860 7 CSGCRSVLLYPRGATNVCCAFCNA 30 **********************97 PP
2	zf-LSD1	49.6	6.4e-16	51	75	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggCrtlL+Y+rGA+sVRC++C+tV Cc06_g12860 51 CGGCRTLLMYTRGATSVRCSCCHTV 75 ************************9 PP
3	zf-LSD1	47.4	3e-15	88	111	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 Cg+Crt+L+YP+GApsV+Ca+C+ Cc06_g12860 88 CGNCRTTLMYPYGAPSVKCAVCHY 111 **********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	3.4E-12	4	32	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.0E-9	7	30	IPR005735	Zinc finger, LSD1-type
SuperFamily	SSF48695	1.95E-5	21	110	IPR011031	Multihaem cytochrome
TIGRFAMs	TIGR01053	1.9E-17	48	77	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.7E-13	51	75	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	9.3E-13	85	114	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.4E-14	88	112	IPR005735	Zinc finger, LSD1-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000303	Biological Process	response to superoxide
GO:0001666	Biological Process	response to hypoxia
GO:0002240	Biological Process	response to molecule of oomycetes origin
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009862	Biological Process	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104	Biological Process	regulation of ethylene-activated signaling pathway
GO:0010310	Biological Process	regulation of hydrogen peroxide metabolic process
GO:0010602	Biological Process	regulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618	Biological Process	aerenchyma formation
GO:0043069	Biological Process	negative regulation of programmed cell death

Sequence ? help Back to Top
Protein Sequence Length: 181 aa Download sequence Send to blast
MQSQIVCSGC RSVLLYPRGA TNVCCAFCNA LTPVPPPQLP PPGMDMAQLI CGGCRTLLMY 60 TRGATSVRCS CCHTVNLAPV SNVAHVNCGN CRTTLMYPYG APSVKCAVCH YITNVNMSNT 120 RVPIPMHQPS GTVTPPLMPS TSSGLAHSQS QTVVVENPMS VDKSGKLVSN VVVGVTTEKK 180 *

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027068829.1	1e-127	protein LSD1-like isoform X2
Refseq	XP_027072988.1	1e-127	protein LSD1-like isoform X2
Refseq	XP_027157190.1	1e-127	protein LSD1-like isoform X2
Refseq	XP_027177290.1	1e-127	protein LSD1-like isoform X2
Swissprot	Q6ASS2	2e-72	LOL3_ORYSJ; Protein LOL3
TrEMBL	A0A068U3V6	1e-126	A0A068U3V6_COFCA; Uncharacterized protein
STRING	XP_008225697.1	9e-99	(Prunus mume)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1679	24	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	3e-72	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]