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.007G028700.3.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: 161aa MW: 16960.4 Da PI: 9.2038

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.007G028700.3.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	29	1.7e-09	7	30	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 CggC+ lL+Y rGA+ V+C+ C+t Sobic.007G028700.3.p 7 CGGCKRLLQYRRGATGVCCPTCNT 30 ***********************9 PP
2	zf-LSD1	31.9	2.2e-10	85	107	1	23
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCd 23 Cg+Crt+L+YP+GA+ V C+ C Sobic.007G028700.3.p 85 CGQCRTTLAYPPGATTVGCPTCR 107 **********************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	1.7E-9	4	32	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	5.6E-8	7	30	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	9.2E-6	44	68	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	6.1E-6	46	67	IPR005735	Zinc finger, LSD1-type
Gene3D	G3DSA:3.30.40.10	7.5E-4	60	111	IPR013083	Zinc finger, RING/FYVE/PHD-type
TIGRFAMs	TIGR01053	2.0E-8	82	111	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	8.8E-10	85	108	IPR005735	Zinc finger, LSD1-type

Sequence ? help Back to Top
Protein Sequence Length: 161 aa Download sequence Send to blast
MHSQLVCGGC KRLLQYRRGA TGVCCPTCNT FTAANPSGPE MSELVCGGCF TMLVHSRSAT 60 NIRCPHCSRL NSTRSAGNQM GHLSCGQCRT TLAYPPGATT VGCPTCRNIN PVRNNHTGGS 120 ARPAPSDARP QTVLVENPKT LDEKGKLVSN VAVGVTSWKR *

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.007G028700.3.p

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_021319997.1	1e-114	protein LOL4 isoform X1
Refseq	XP_021319998.1	1e-114	protein LOL4 isoform X1
Swissprot	Q84UR0	2e-70	LOL4_ORYSJ; Protein LOL4
TrEMBL	A0A1Z5R7R9	1e-113	A0A1Z5R7R9_SORBI; Uncharacterized protein
STRING	Si014280m	1e-96	(Setaria italica)
STRING	Sb07g002500.1	9e-98	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP12333	29	38
Representative plant	OGRP1146	17	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	7e-37	LSD family protein

Link Out ? help Back to Top
Phytozome	Sobic.007G028700.3.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]