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

LOC_Os02g57490.1

Common Name

LOC4331170, OJ1202_E07.33, Os02g0820500, OSNPB_020820500, P0474F11.14

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa

Family

LBD

Protein Properties

Length: 217aa MW: 22457.6 Da PI: 7.9346

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os02g57490.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	121.9	3.5e-38	21	121	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlka 92 +C aCk+lrr+C+++Cv+apyf +eq +++fa++hk+FGasn +kll++lp +r +a+ +++yeA+ar+rdPvyG+v+ i++lqqq++ l+a LOC_Os02g57490.1 21 PCGACKFLRRRCVPECVFAPYFSSEQgAARFAAIHKVFGASNASKLLSHLPVADRCEAVVTITYEAQARLRDPVYGCVAQIFALQQQVAILQA 113 7*********************9989************************************************************* PP DUF260 93 elallkee 100 +l +++++ LOC_Os02g57490.1 114 QLMQARAQ 121 999987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.951	20	122	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.2E-37	21	119	IPR004883	Lateral organ boundaries, LOB

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

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009005	anatomy	root

Sequence ? help Back to Top
Protein Sequence Length: 217 aa Download sequence Send to blast
MAGATAAGAA AAAAGTGAGS PCGACKFLRR RCVPECVFAP YFSSEQGAAR FAAIHKVFGA 60 SNASKLLSHL PVADRCEAVV TITYEAQARL RDPVYGCVAQ IFALQQQVAI LQAQLMQARA 120 QLACGIQSSS HSPVSWPDSG SISALLRQDM ARRPPGGALD DCFGGGGALL PELMAAGFKD 180 DVAAVQMQQH CSKAVDAGEL QYLAQAMMRS TSNYSQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-39	11	125	1	117	LOB family transfactor Ramosa2.1
5ly0_B	7e-39	11	125	1	117	LOB family transfactor Ramosa2.1
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.7342	0.0	callus\| root

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	32974205	0.0
Expression Atlas	Q6K713	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269\|PubMed:19717544}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots and faintly in shoots. {ECO:0000269\|PubMed:12068116}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:26059335}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00309	DAP	Transfer from AT2G42430	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os02g57490.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:23749813}.

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os02g57490

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK064187	0.0	AK064187.1 Oryza sativa Japonica Group cDNA clone:002-104-C02, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015626197.1	1e-155	LOB domain-containing protein 16
Swissprot	Q9SLB7	2e-59	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A0D9Z098	1e-154	A0A0D9Z098_9ORYZ; Uncharacterized protein
TrEMBL	A0A0E0GEZ6	1e-154	A0A0E0GEZ6_ORYNI; Uncharacterized protein
TrEMBL	A0A0E0NMY5	1e-154	A0A0E0NMY5_ORYRU; Uncharacterized protein
TrEMBL	A2XB42	1e-154	A2XB42_ORYSI; Uncharacterized protein
TrEMBL	I1P5M2	1e-154	I1P5M2_ORYGL; Uncharacterized protein
TrEMBL	Q6K713	1e-154	Q6K713_ORYSJ; LOB domain protein-like
STRING	OGLUM02G38740.1	1e-155	(Oryza glumipatula)
STRING	ORUFI02G39110.1	1e-155	(Oryza rufipogon)
STRING	OS02T0820500-01	1e-155	(Oryza sativa)
STRING	ONIVA02G40360.1	1e-155	(Oryza nivara)
STRING	ORGLA02G0327800.1	1e-155	(Oryza glaberrima)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10599	34	43
Representative plant	OGRP405	15	100

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42430.1	6e-45	lateral organ boundaries-domain 16

Link Out ? help Back to Top
Phytozome	LOC_Os02g57490.1
Entrez Gene	4331170

Publications ? help Back to Top
Bargmann BO,Birnbaum KD,Brenner ED An undergraduate study of two transcription factors that promote lateral root formation. Biochem Mol Biol Educ, 2014 May-Jun. 42(3): p. 237-45 [PMID:24615800] Cabrera J,Fenoll C,Escobar C Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis. Plant Signal Behav, 2015. 10(3): p. e990825 [PMID:25664644] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Jeon E, et al. LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis. Plant Cell Physiol., 2017. 58(12): p. 2190-2201 [PMID:29040694] 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] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751] Liu J, et al. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. Plant Cell Physiol., 2018. 59(4): p. 734-743 [PMID:29361138] 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]