PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera

Family

LBD

Protein Properties

Length: 263aa MW: 26964.3 Da PI: 8.067

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bostr.25993s0233.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.5	3e-40	37	137	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqle 88 +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdP+yG+v++i++lqqq+ Bostr.25993s0233.1.p 37 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGASNVSKLLLHIPVHRRSDAVVTICYEAQARIRDPIYGCVAHIFALQQQVV 125 7*********************998899******************************************************* PP DUF260 89 qlkaelallkee 100 +l+ae+++l+++ Bostr.25993s0233.1.p 126 NLQAEVSYLQAH 137 *****99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF038127	2.4E-131	1	262	IPR017394	LOB domain-containing protein 18/20
PROSITE profile	PS50891	22.866	36	138	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.9E-39	37	135	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 263 aa Download sequence Send to blast
MSGGGNTITA VGGGGGGCGG GGSSGGGGSS GSGGGGPCGA CKFLRRKCVP GCIFAPYFDS 60 EQGSAYFAAV HKVFGASNVS KLLLHIPVHR RSDAVVTICY EAQARIRDPI YGCVAHIFAL 120 QQQVVNLQAE VSYLQAHLAS LELPQPQTRL PPLSQPQPLF FTPPPPFSIT DLPASVSPLP 180 STYDLASIFD QTASASAWAT QQRRIVDPRQ QYGVSSSSSS AAAIGLGGGN SDLQALAHEL 240 LHRQGSPPPA ATDDSPSRSM SR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-39	33	138	7	111	LOB family transfactor Ramosa2.1
5ly0_B	4e-39	33	138	7	111	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:23872272, ECO:0000269\|PubMed:26059335}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00314	DAP	Transfer from AT2G45420	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Bostr.25993s0233.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:23749813}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473853	0.0	AB473853.1 Arabidopsis thaliana ASL20 mRNA for ASYMMETRIC LEAVES2-like 20 protein, complete cds.
GenBank	AF447891	0.0	AF447891.1 Arabidopsis thaliana LOB DOMAIN 18 (LBD18) mRNA, complete cds.
GenBank	BT025716	0.0	BT025716.1 Arabidopsis thaliana At2g45420 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010508173.1	1e-152	PREDICTED: LOB domain-containing protein 18
Swissprot	O22131	1e-128	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	V4N211	1e-142	V4N211_EUTSA; Uncharacterized protein
STRING	Bostr.25993s0233.1.p	0.0	(Boechera stricta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45420.1	1e-107	LOB domain-containing protein 18

Link Out ? help Back to Top
Phytozome	Bostr.25993s0233.1.p

Publications ? help Back to Top
Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Lee HW, et al. Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation. Plant Physiol., 2017. 174(1): p. 301-311 [PMID:28336771] Pandey SK,Kim J Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis. Plant Signal Behav, 2018. 13(1): p. e1411450 [PMID:29227192] Pandey SK, et al. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. Plant J., 2018. 95(2): p. 233-251 [PMID:29681137] Lee HW, et al. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC Plant Biol., 2019. 19(1): p. 46 [PMID:30704405]