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

RrC14353_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 238aa MW: 25820.7 Da PI: 7.6251

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC14353_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	118.6	3.5e-37	15	115	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 +C aCk+lrrkC +dC++a yf +eq +++fa++hk+FGasnv+kll ++p ++r +a+ +++yeA+ar++dPvyG+v++i++lqqq++ l+a++ ++ RrC14353_p1 15 PCGACKFLRRKCLSDCIFATYFSSEQgAARFAAIHKVFGASNVSKLLLNVPIHDRFEAVVTIAYEAQARLHDPVYGCVSHIFSLQQQVAYLQAQVMQM 112 7*********************9989****************************************************************9988 PP DUF260 98 kee 100 k++ RrC14353_p1 113 KAH 115 876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.998	14	116	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.0E-36	15	113	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 238 aa Download sequence Send to blast
MATSGNSTTA GTGSPCGACK FLRRKCLSDC IFATYFSSEQ GAARFAAIHK VFGASNVSKL 60 LLNVPIHDRF EAVVTIAYEA QARLHDPVYG CVSHIFSLQQ QVAYLQAQVM QMKAHIAGHQ 120 TSAAEGTHQF ETWQQTSGSL IDGAYSIPYN HHNHTYYGHI SPNNPVSSQS SLEESFSNTS 180 SDVTTTANTR ETHQTGGGVY GKGDLGFQEG FPNKKRSVSY CNSDLGELQA LALRIMKN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	9e-38	7	109	3	104	LOB family transfactor Ramosa2.1
5ly0_B	9e-38	7	109	3	104	LOB family transfactor Ramosa2.1
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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}.

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	AC241104	1e-174	AC241104.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH017L09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009133536.1	1e-163	PREDICTED: LOB domain-containing protein 16-like
Refseq	XP_013681149.1	1e-163	LOB domain-containing protein 16-like
Refseq	XP_013724346.1	1e-163	LOB domain-containing protein 16-like
Swissprot	Q9SLB7	1e-147	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A291LR07	1e-162	A0A291LR07_BRARR; Transcription factor LBD16b
TrEMBL	A0A397ZY86	1e-162	A0A397ZY86_BRACM; Uncharacterized protein
TrEMBL	M4C7S9	1e-162	M4C7S9_BRARP; Uncharacterized protein
STRING	Bra000257.1-P	1e-163	(Brassica rapa)

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
AT2G42430.1	1e-116	lateral organ boundaries-domain 16

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]