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

AT4G00220.1

Common Name

ASL19, F6N15.4, JLO, LBD30

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

LBD

Protein Properties

Length: 228aa MW: 23968.1 Da PI: 7.2496

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G00220.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	132.4	1.8e-41	17	117	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll+++pe++r+da+ s+++eA+ar+rdP+yG+v++i +lqqq+ +l++el++l AT4G00220.1 17 PCGACKFLRRKCVAGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLHHVPEHKRPDAVVSICFEAQARLRDPIYGCVSHIVSLQQQVVSLQTELSYL 114 7*********************9989******************************************************************99 PP DUF260 98 kee 100 +++ AT4G00220.1 115 QAH 117 986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.688	16	118	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	8.8E-40	17	115	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010199	Biological Process	organ boundary specification between lateral organs and the meristem

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000019	anatomy	gynoecium primordium
PO:0000229	anatomy	flower meristem
PO:0000230	anatomy	inflorescence meristem
PO:0000290	anatomy	tracheary element
PO:0004704	anatomy	sepal primordium
PO:0004705	anatomy	stamen primordium
PO:0009046	anatomy	flower
PO:0020003	anatomy	plant ovule
PO:0007611	developmental stage	petal differentiation and expansion stage

Sequence ? help Back to Top
Protein Sequence Length: 228 aa Download sequence Send to blast
MSSSGNPSSS SGGGGGPCGA CKFLRRKCVA GCIFAPYFDS EQGAAHFAAV HKVFGASNVS 60 KLLHHVPEHK RPDAVVSICF EAQARLRDPI YGCVSHIVSL QQQVVSLQTE LSYLQAHLAT 120 LELPQPQPPQ VPVSSSGSLQ ALSITDLPTI SPSVYDLSSI FEPVMSSTWA MQQQPRPSDH 180 LFGVPSSSNM GGGGELQALA REFIHGGQMP AQPSPGTSGS ASSVIKRE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-38	10	118	4	111	LOB family transfactor Ramosa2.1
5ly0_B	1e-38	10	118	4	111	LOB family transfactor Ramosa2.1
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.21182	0.0	flower\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30678570	0.0
Genevisible	255701_at	0.0
Expression Atlas	AT4G00220	-
AtGenExpress	AT4G00220	-
ATTED-II	AT4G00220	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, stems, leaves and flowers (PubMed:12068116). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269\|PubMed:12068116, ECO:0000269\|PubMed:19088331}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a protein containing a LOB domain that is expressed in embryos, flower primordium and lateral floral organ boundaries. Overexpression is correlated with activation of STM and KNAT1 and down regulation of PIN1 and reduced auxin transport levels. Ectopic expression in plants results in premature termination of the shoot apical meristem and small, lobed leaves.
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. {ECO:0000269\|PubMed:19088331}.

Function -- GeneRIF ? help Back to Top
Jagged Lateral Organs (JLO) acts from the boundary to orchestrate the drastic changes in gene expression that entail the initiation of plant lateral organs. [JLO] [PMID: 17557810] ASL19 were expressed in immature tracheary elements (TEs), and the expression was dependent on VASCULAR-RELATED NAC-DOMAIN PROTEIN6 (VND6) and VND7, which are transcription factors required for TE differentiation. [PMID: 19088331] JLO is a central regulator of auxin distribution and signaling throughout plant development. [PMID: 20852917] The JLO and AS2 proteins interact molecularly and form multimeric complexes with AS1 to suppress KNOX expression. AS2 together with JLO regulate auxin transport in seedling roots. [PMID: 22822207] Data indicate that the transcript levels of HAK5 and four transcriptin factor genes DDF2, JLO, bHLH121 and TFII_A were highly up-regulated in response to both -K and salt stress. [PMID: 23825216] JLO can regulate auxin perception and consequently auxin transport and auxin-responsive gene expression [PMID: 28472464] Genes controlling SCW formation were activated by the overexpression of LBD30, but not in the LBD30(K226R) mutant. LBD30 enhancement of SCW formation resulted from upregulation of SND1/NST1-mediated transcriptional networks. This study presents a mechanism by which sumoylation of LBD30, mediated by SIZ1, regulates SCW formation in A. thaliana. [PMID: 30657769]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G00220.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G23080(R), AT1G62360(A), AT1G70940(R), AT1G73590(R), AT2G01420(R), AT2G37630(R), AT4G08150(A), AT4G34160(A), AT5G67260(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G65620

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G00220

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473852	0.0	AB473852.1 Arabidopsis thaliana ASL19 mRNA for ASYMMETRIC LEAVES2-like 19 protein, complete cds.
GenBank	AF432232	0.0	AF432232.1 Arabidopsis thaliana LOB DOMAIN 30 (LBD30) mRNA, complete cds.
GenBank	BT026407	0.0	BT026407.1 Arabidopsis thaliana At4g00220 mRNA, complete cds.
GenBank	DQ446787	0.0	DQ446787.1 Arabidopsis thaliana clone pENTR221-At4g00220 LOB domain protein 30/lateral organ boundaries domain protein 30 (At4g00220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191933.1	1e-165	Lateral organ boundaries (LOB) domain family protein
Swissprot	O81323	1e-166	LBD30_ARATH; LOB domain-containing protein 30
TrEMBL	A0A178UUM7	1e-163	A0A178UUM7_ARATH; LBD30
STRING	AT4G00220.1	1e-164	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359
Representative plant	OGRP405	15	100

Link Out ? help Back to Top
Phytozome	AT4G00220.1
Entrez Gene	828084
iHOP	AT4G00220
wikigenes	AT4G00220

Publications ? help Back to Top
Iwakawa H, et al. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper. Plant Cell Physiol., 2002. 43(5): p. 467-78 [PMID:12040093] Shuai B,Reynaga-Peña CG,Springer PS The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol., 2002. 129(2): p. 747-61 [PMID:12068116] Underwood BA,Vanderhaeghen R,Whitford R,Town CD,Hilson P Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations. Plant Biotechnol. J., 2006. 4(3): p. 317-24 [PMID:17147637] Borghi L,Bureau M,Simon R Arabidopsis JAGGED LATERAL ORGANS is expressed in boundaries and coordinates KNOX and PIN activity. Plant Cell, 2007. 19(6): p. 1795-808 [PMID:17557810] Soyano T,Thitamadee S,Machida Y,Chua NH ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. Plant Cell, 2008. 20(12): p. 3359-73 [PMID:19088331] Matsumura Y,Iwakawa H,Machida Y,Machida C Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Plant J., 2009. 58(3): p. 525-37 [PMID:19154202] Bureau M,Simon R JLO regulates embryo patterning and organ initiation by controlling auxin transport. Plant Signal Behav, 2008. 3(2): p. 145-7 [PMID:19704738] Bureau M,Rast MI,Illmer J,Simon R JAGGED LATERAL ORGAN (JLO) controls auxin dependent patterning during development of the Arabidopsis embryo and root. Plant Mol. Biol., 2010. 74(4-5): p. 479-91 [PMID:20852917] Hsieh TF, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 1755-62 [PMID:21257907] Rast MI,Simon R Arabidopsis JAGGED LATERAL ORGANS acts with ASYMMETRIC LEAVES2 to coordinate KNOX and PIN expression in shoot and root meristems. Plant Cell, 2012. 24(7): p. 2917-33 [PMID:22822207] Meinke DW A survey of dominant mutations in Arabidopsis thaliana. Trends Plant Sci., 2013. 18(2): p. 84-91 [PMID:22995285] Hong JP, et al. Identification and characterization of transcription factors regulating Arabidopsis HAK5. Plant Cell Physiol., 2013. 54(9): p. 1478-90 [PMID:23825216] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Rast-Somssich MI, et al. The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J. Exp. Bot., 2017. 68(11): p. 2741-2755 [PMID:28472464] Liu C,Yu H,Li L SUMO modification of LBD30 by SIZ1 regulates secondary cell wall formation in Arabidopsis thaliana. PLoS Genet., 2019. 15(1): p. e1007928 [PMID:30657769]