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

Pavir.9KG589300.1.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

LBD

Protein Properties

Length: 181aa MW: 18567.9 Da PI: 6.2264

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.9KG589300.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	120.3	1.1e-37	14	114	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 +C aCk+lrrkC+++Cv+ap+f+ae+ +++fa++hk+FGasn kll+++ + +r++a+++++yeA+ar+rdP+yG+v++i++lqqq+++ Pavir.9KG589300.1.p 14 PCGACKFLRRKCPAECVFAPHFCAEDgAAQFAAIHKVFGASNAAKLLQQVAPADRSEAAATVTYEAQARLRDPIYGCVAHIFALQQQVAS 103 7*********************9989********************************************************** PP DUF260 90 lkaelallkee 100 l+ ++ ++k++ Pavir.9KG589300.1.p 104 LQMQVLQAKAQ 114 *99888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.508	13	115	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	9.4E-37	14	111	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 181 aa Download sequence Send to blast
MASSGSGGGA PGSPCGACKF LRRKCPAECV FAPHFCAEDG AAQFAAIHKV FGASNAAKLL 60 QQVAPADRSE AAATVTYEAQ ARLRDPIYGC VAHIFALQQQ VASLQMQVLQ AKAQVAQTMA 120 AAGGAQAAGS PLLQRWPLEP ESLSTQSSGC YSAPSCDGSA ALQEMYCGGF GEQEEGSYTR 180 *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	2e-32	12	117	9	113	LOB family transfactor Ramosa2.1
5ly0_B	2e-32	12	117	9	113	LOB family transfactor Ramosa2.1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.33736	0.0	root

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	Pavir.9KG589300.1.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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF051734	0.0	EF051734.1 Zea mays RTCN mRNA, complete cds.
GenBank	KJ728375	0.0	KJ728375.1 Zea mays clone pUT6657 LOB transcription factor (LOB21) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004985693.1	1e-109	LOB domain-containing protein 16
Swissprot	Q9SLB7	1e-53	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	K4AFS0	1e-107	K4AFS0_SETIT; Uncharacterized protein
STRING	Pavir.Ib00282.1.p	1e-126	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10262	33	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	7e-43	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	Pavir.9KG589300.1.p

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]