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_013635009.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 251aa MW: 25911.1 Da PI: 8.2887

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013635009.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.2	3.6e-40	34	134	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l+ae+ XP_013635009.1 34 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGASNVSKLLLHIPVHRRADAVVTICYEAQARIRDPIYGCVAHIFALQQQVVNLQAEV 128 7*********************998899*************************************************************** PP DUF260 95 allkee 100 ++l+++ XP_013635009.1 129 SYLQAH 134 *99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.8	33	135	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.8E-39	34	132	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 251 aa Download sequence Send to blast
MSGGGNTITS VGGGGCGGGS SSGGGGSSGG GGGPCGACKF LRRKCVPGCI FAPYFDSEQG 60 SAYFAAVHKV FGASNVSKLL LHIPVHRRAD AVVTICYEAQ ARIRDPIYGC VAHIFALQQQ 120 VVNLQAEVSY LQAHLASLEL PQPQTRPPPL TQPQPLFFTP PPPLSITDLP ASVSPYDLAS 180 IVDPPTSWAT QQRRFVDPRN QYGGSSSSSS AAVGLGGGNS DLQALAHELL HRQGSPPPAA 240 TDGSPSRSMS R

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	8e-39	27	135	4	111	LOB family transfactor Ramosa2.1
5ly0_B	8e-39	27	135	4	111	LOB family transfactor Ramosa2.1
Search in ModeBase

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, stems, leaves and flowers (PubMed:12068116, PubMed:24484953). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269\|PubMed:12068116, ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:24484953}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013635009.1

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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC189498	0.0	AC189498.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB086L12, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013635009.1	0.0	PREDICTED: LOB domain-containing protein 18
Swissprot	O22131	1e-117	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A0D3BQ34	1e-180	A0A0D3BQ34_BRAOL; Uncharacterized protein
STRING	Bo4g024620.1	0.0	(Brassica oleracea)

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-109	LOB domain-containing protein 18

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]