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

Bradi3g55680.1.p

Common Name

BRADI_3g55680, LOC100823689

Organism

Brachypodium distachyon

Taxonomic ID

15368

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium

Family

LBD

Protein Properties

Length: 210aa MW: 21861.9 Da PI: 8.0256

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bradi3g55680.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	115.4	3.6e-36	16	117	1	101
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlka 92 +C aCk+lrr+C+++Cv+apyf +e+ +++fa++hk+FGasn kll++lp er +a+ ++++eA+ r+rdPvyG+v+ i++lqqq++ l+a Bradi3g55680.1.p 16 PCGACKFLRRRCVAECVFAPYFSSEHgASRFAAIHKVFGASNAAKLLAHLPAAERCEAVVTITFEAQSRLRDPVYGCVAQIFALQQQVAILQA 108 7*******************999979************************************************************* PP DUF260 93 elallkeel 101 +l ++k++l Bradi3g55680.1.p 109 QLMQAKAQL 117 9999875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.46	15	117	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.5E-35	16	114	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: 210 aa Download sequence Send to blast
MAAGAGGVGA AGAGSPCGAC KFLRRRCVAE CVFAPYFSSE HGASRFAAIH KVFGASNAAK 60 LLAHLPAAER CEAVVTITFE AQSRLRDPVY GCVAQIFALQ QQVAILQAQL MQAKAQLACG 120 IQSTSPAASL ISQQHHHHHQ WPDSASSISA LLRQQEGSGF GGAATLPELM GGDGVTPMSS 180 MQQHCSKVDG GELQYLAQAM MRSPNYSGF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-35	12	120	7	117	LOB family transfactor Ramosa2.1
5ly0_B	1e-35	12	120	7	117	LOB family transfactor Ramosa2.1
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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	Bradi3g55680.1.p

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	AK368515	1e-133	AK368515.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv2075A19.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003572959.1	1e-151	LOB domain-containing protein 16
Swissprot	Q9SLB7	4e-57	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	I1IE14	1e-150	I1IE14_BRADI; Uncharacterized protein
STRING	BRADI3G55680.1	1e-150	(Brachypodium distachyon)

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	2e-41	lateral organ boundaries-domain 16

Link Out ? help Back to Top
Phytozome	Bradi3g55680.1.p
Entrez Gene	100823689

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]