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

Rsa1.0_56503.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 75aa MW: 6911.62 Da PI: 8.6653

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_56503.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	52.2	1.8e-16	35	75	1	40
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGas 40 +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGas Rsa1.0_56503.1_g00001.1 35 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGAS 75 7*********************998899*******86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	15.066	34	75	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	5.5E-15	35	75	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 75 aa Download sequence Send to blast
MSGGGNTITA VGGGGSGGGS SGGGGGSSSG GGGGPCGACK FLRRKCVPGC IFAPYFDSEQ 60 GSAYFAAVHK VFGAS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-18	25	75	1	50	LOB family transfactor Ramosa2.1
5ly0_B	4e-18	25	75	1	50	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	Rsa1.0_56503.1_g00001.1

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	AC189498	2e-71	AC189498.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB086L12, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018440274.1	5e-42	PREDICTED: LOB domain-containing protein 18
Swissprot	O22131	4e-25	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A1J3GN27	1e-30	A0A1J3GN27_NOCCA; LOB domain-containing protein 18 (Fragment)
STRING	Bostr.25993s0233.1.p	5e-27	(Boechera stricta)
STRING	XP_006295913.1	6e-27	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45420.1	8e-25	LOB domain-containing protein 18

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]