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

Sobic.008G165000.1.p

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

LSD

Protein Properties

Length: 262aa MW: 27626.3 Da PI: 8.9076

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.008G165000.1.p	genome	JGI	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	91	115	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCrt+L YPrGApsV+Ca+C++V Sobic.008G165000.1.p 91 CHGCRTVLLYPRGAPSVCCAVCHAV 115 ************************9 PP
2	zf-LSD1	40.1	5.9e-13	130	154	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 CggC+tlL+Y+r A+ VRC++CdtV Sobic.008G165000.1.p 130 CGGCQTLLMYTRSATTVRCSCCDTV 154 ************************9 PP
3	zf-LSD1	50.1	4.5e-16	168	192	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+C+t+L+YP+GApsV+Ca+C+++ Sobic.008G165000.1.p 168 CGQCQTVLMYPYGAPSVKCAICNFI 192 ***********************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	5.7E-13	88	118	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.8E-11	91	115	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	7.8E-13	128	157	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.2E-10	130	154	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	1.7E-11	165	194	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	4.0E-14	168	192	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 262 aa Download sequence Send to blast
MFRCLAGGMG RVRRSVAGSI NRAGEHGRSV WGNRMACAGF GIGRSWRGLF FSPDGAKLIE 60 TLIVDVCWCK KNRIELGVGL GWDSMQSQIV CHGCRTVLLY PRGAPSVCCA VCHAVTNVPP 120 PAIEMARLIC GGCQTLLMYT RSATTVRCSC CDTVNLVRPV SSIAHVNCGQ CQTVLMYPYG 180 APSVKCAICN FITNVGGVTP VRPLPPALPA SSGNSYSIPS TSVPMNQSQN VTVVVENPMT 240 VDDKGKLVSN VVVGVTSGGK K*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.6388	0.0	callus\| leaf\| pollen\| root

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.008G165000.1.p

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	JN983231	0.0	JN983231.1 Miscanthus sinensis clone MSIL000019 putative zinc finger LOL2 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001132871.1	1e-125	uncharacterized protein LOC100194364
Swissprot	Q2QMB3	4e-94	LOL2_ORYSJ; Protein LOL2
TrEMBL	A0A1B6PE69	0.0	A0A1B6PE69_SORBI; Uncharacterized protein
STRING	GRMZM2G114613_P02	1e-125	(Zea mays)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1347	38	124
Representative plant	OGRP1146	17	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32540.1	4e-54	lsd one like 1

Link Out ? help Back to Top
Phytozome	Sobic.008G165000.1.p

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] Wu J, et al. OsLOL1, a C2C2-type zinc finger protein, interacts with OsbZIP58 to promote seed germination through the modulation of gibberellin biosynthesis in Oryza sativa. Plant J., 2014. 80(6): p. 1118-30 [PMID:25353370]