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

LOC_Os03g05500.1

Common Name

CRLL1, LOC4331627, Os03g0149000, OSNPB_030149000

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa

Family

LBD

Protein Properties

Length: 186aa MW: 19631 Da PI: 6.4849

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os03g05500.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	123.3	1.2e-38	13	113	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlka 92 +C aCk+lrrkCa++Cv+apyf+ae+ +++fa++hk+FGasn kll+++ + +r++++++++yeA+ar+rdPvyG+v++i++lqqql++l++ LOC_Os03g05500.1 13 PCGACKFLRRKCAAECVFAPYFCAEDgAAQFAAIHKVFGASNAAKLLQQVAPGDRSEVAATVTYEAQARLRDPVYGCVAHIFALQQQLATLQV 105 7*********************9989************************************************************* PP DUF260 93 elallkee 100 ++a++k++ LOC_Os03g05500.1 106 QVAQAKTQ 113 *99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.791	12	114	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	3.0E-37	13	111	IPR004883	Lateral organ boundaries, LOB

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009005	anatomy	root

Sequence ? help Back to Top
Protein Sequence Length: 186 aa Download sequence Send to blast
MASSGVGGVP GSPCGACKFL RRKCAAECVF APYFCAEDGA AQFAAIHKVF GASNAAKLLQ 60 QVAPGDRSEV AATVTYEAQA RLRDPVYGCV AHIFALQQQL ATLQVQVAQA KTQVAQTLAA 120 AGMLTAGNPL LQHQQQQQQA WQIEHESTMT STQSSGCYSA PRSDGSTSLQ DMYCFGEQEE 180 GSYSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-33	11	114	9	111	LOB family transfactor Ramosa2.1
5ly0_B	1e-33	11	114	9	111	LOB family transfactor Ramosa2.1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.81319	0.0	root

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	Q5KQR7

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	LOC_Os03g05500.1

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	-

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os03g05500

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB200235	0.0	AB200235.1 Oryza sativa Japonica Group CRLL1 mRNA for LOB domain protein, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015632118.1	1e-133	LOB domain-containing protein 16
Swissprot	Q9SLB7	4e-52	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	I1P7L2	1e-132	I1P7L2_ORYGL; Uncharacterized protein
TrEMBL	Q5KQR7	1e-132	Q5KQR7_ORYSJ; Expressed protein
STRING	OS03T0149000-01	1e-133	(Oryza sativa)
STRING	ORGLA03G0035800.1	1e-133	(Oryza glaberrima)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10262	33	44
Representative plant	OGRP405	15	100

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	1e-37	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	LOC_Os03g05500.1
Entrez Gene	4331627

Publications ? help Back to Top
Inukai Y, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling. Plant Cell, 2005. 17(5): p. 1387-96 [PMID:15829602] 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]