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

Seita.9G282200.1.p

Organism

Setaria italica

Taxonomic ID

4555

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 263aa MW: 27185.7 Da PI: 6.8581

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Seita.9G282200.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.5	2.9e-40	34	134	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleql 90 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p+++r da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l Seita.9G282200.1.p 34 PCGACKFLRRKCVSGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLQIPPHKRLDAVVTVCYEAQARLRDPIYGCVSHIFALQQQVVNL 124 7*********************9989*********************************************************** PP DUF260 91 kaelallkee 100 +ael +l+ + Seita.9G282200.1.p 125 QAELTYLQGH 134 **998865 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.376	33	135	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.5E-39	34	132	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 263 aa Download sequence Send to blast
MSSSVAGASA GGGAGGLGGG GGAGAGAGIG GGGPCGACKF LRRKCVSGCI FAPYFDSEQG 60 AAHFAAVHKV FGASNVSKLL LQIPPHKRLD AVVTVCYEAQ ARLRDPIYGC VSHIFALQQQ 120 VVNLQAELTY LQGHLTTMEL PTPPPFAPQP QPPMPTNAAF SVSNLPLSSS VPATVDLSTL 180 LDPHNQSQQW AFQFQQQQVL QQQQQLLQQQ QYMQMGEGSS RVAGGSSTAD GGDLQALARE 240 LLDRHGMVAA GSPPEPPTPA IQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-39	30	128	7	104	LOB family transfactor Ramosa2.1
5ly0_B	4e-39	30	128	7	104	LOB family transfactor Ramosa2.1
Search in ModeBase

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	Seita.9G282200.1.p

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	BT061431	1e-124	BT061431.1 Zea mays full-length cDNA clone ZM_BFb0145J09 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004986691.1	0.0	LOB domain-containing protein 18-like
Swissprot	O22131	6e-70	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A368SLP7	0.0	A0A368SLP7_SETIT; Uncharacterized protein
STRING	Pavir.Ib02517.1.p	1e-97	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP3346	37	82

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45420.1	5e-62	LOB domain-containing protein 18

Link Out ? help Back to Top
Phytozome	Seita.9G282200.1.p

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]