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

XP_009142063.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 246aa MW: 26618.6 Da PI: 8.0286

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009142063.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	121.5	4.5e-38	15	115	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkCa+dC++apyf +eq +++fa++hk+FGasnv+kll ++p ++r +a+ +++yeA+ar +dPvyG+v++i++lqqq++ l+a++ XP_009142063.1 15 PCGACKFLRRKCASDCIFAPYFSSEQgAARFAAIHKVFGASNVSKLLLNVPIHDRCEAVVTIAYEAQARRHDPVYGCVSHIFALQQQVAYLQAQV 109 7*********************9989****************************************************************9 PP DUF260 95 allkee 100 ++k++ XP_009142063.1 110 MQMKAQ 115 999887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.8	14	116	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.6E-37	15	113	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

Sequence ? help Back to Top
Protein Sequence Length: 246 aa Download sequence Send to blast
MATSGNDTTT GTGSPCGACK FLRRKCASDC IFAPYFSSEQ GAARFAAIHK VFGASNVSKL 60 LLNVPIHDRC EAVVTIAYEA QARRHDPVYG CVSHIFALQQ QVAYLQAQVM QMKAQIAGHQ 120 TSAAGDLRNS SESTHQQYMT CQQTTGSPIG NAYSTAYNHH HQPYYGHVNP NNPVSPQSSL 180 EETFSNTSSD VTTTANVRET QQTGGGVYGH GGLGFHEGYP NKKRSVSYCN SDLGELQALA 240 LRMMKN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-36	8	109	4	104	LOB family transfactor Ramosa2.1
5ly0_B	1e-36	8	109	4	104	LOB family transfactor Ramosa2.1
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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	XP_009142063.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473851	0.0	AB473851.1 Arabidopsis thaliana ASL18 mRNA for ASYMMETRIC LEAVES2-like 18 protein, complete cds.
GenBank	AF345339	0.0	AF345339.1 Arabidopsis thaliana MHK10.15/At2g42430 mRNA, complete cds.
GenBank	AF410334	0.0	AF410334.1 Arabidopsis thaliana At2g42430/MHK10.15 mRNA, complete cds.
GenBank	AF447890	0.0	AF447890.1 Arabidopsis thaliana LOB DOMAIN 16 (LBD16) mRNA, complete cds.
GenBank	BT000866	0.0	BT000866.1 Arabidopsis thaliana At2g42430/MHK10.15 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009142063.1	0.0	PREDICTED: LOB domain-containing protein 16-like
Swissprot	Q9SLB7	1e-165	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A291LR02	0.0	A0A291LR02_BRARR; Transcription factor LBD16
TrEMBL	M4DK49	0.0	M4DK49_BRARP; Uncharacterized protein
STRING	Bra016877.1-P	0.0	(Brassica rapa)

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
AT2G42430.1	1e-132	lateral organ boundaries-domain 16

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]