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

Solyc06g083930.1.1

Common Name

LOC101261338

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

LBD

Protein Properties

Length: 197aa MW: 21610.2 Da PI: 6.9871

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc06g083930.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	124.3	6e-39	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleql 90 +C aCk+lrrkCa dC++apyf +e+ p+kfa++hk+FGasnv+kll+++p+++r da+ ++ yeA+ar++dPvyG+v+ i++lqqq++ l Solyc06g083930.1.1 7 PCGACKFLRRKCAVDCIFAPYFNSEEgPSKFAAIHKVFGASNVSKLLHNVPTDDRCDAVVTISYEAQARIKDPVYGCVANIFALQQQVAYL 97 7*******************998889*********************************************************** PP DUF260 91 kaelallkee 100 +++l ++k + Solyc06g083930.1.1 98 QSQLMQVKGQ 107 **999876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.527	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.2E-38	7	104	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 197 aa Download sequence Send to blast
MASSGSPCGA CKFLRRKCAV DCIFAPYFNS EEGPSKFAAI HKVFGASNVS KLLHNVPTDD 60 RCDAVVTISY EAQARIKDPV YGCVANIFAL QQQVAYLQSQ LMQVKGQLAQ SLMNSNNCYN 120 PQWINNNINM TSSSGQMTSS SFPANYPNYI NLKSNSSPQS SSMESVDHYS DGHGIMNMQD 180 IQSLDHFLYQ PYNTSS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	9e-40	3	101	7	104	LOB family transfactor Ramosa2.1
5ly0_B	9e-40	3	101	7	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc06g083930.1.1

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	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004242534.1	1e-145	LOB domain-containing protein 16
Swissprot	Q9SLB7	1e-61	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A3Q7H204	1e-143	A0A3Q7H204_SOLLC; Uncharacterized protein
STRING	Solyc06g083930.1.1	1e-144	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA43	24	669
Representative plant	OGRP405	15	100

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42430.1	4e-62	lateral organ boundaries-domain 16

Link Out ? help Back to Top
Phytozome	Solyc06g083930.1.1
Entrez Gene	101261338

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] 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]