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_08090.1_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: 243aa MW: 26085.5 Da PI: 8.0788

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_08090.1_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	59.9	7.3e-19	15	63	1	48
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllka 48 +C aCk+lrrkCa+dC++apyf +eq +++fa++hk+FGasnv+++l+ Rsa1.0_08090.1_g00001.1 15 PCGACKFLRRKCASDCIFAPYFSSEQgAARFAAIHKVFGASNVSNVLEP 63 7*********************9989***************9985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	14.245	14	121	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.3E-17	15	63	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 243 aa Download sequence Send to blast
MATSGNSTTA GTGSPCGACK FLRRKCASDC IFAPYFSSEQ GAARFAAIHK VFGASNVSNV 60 LEPATCLSSC SMSLSMIDVK LLSPSPTKLR LVFMILFMAV AYLQAQVMQM KVQIGGHQTS 120 AAGDLRNSSE STQEFMTWQQ SSGSPMGSAY AIPYDHHHHP YYGHVNPNNP ILQQSSPEES 180 LSSTSSDVTT TANLRETHQT GAGVYGHGGL GFHEGYPSKK RPVSYCNSDL GELQALALRM 240 MKN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	2e-17	8	61	4	56	LOB family transfactor Ramosa2.1
5ly0_B	2e-17	8	61	4	56	LOB family transfactor Ramosa2.1
Search in ModeBase

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	Rsa1.0_08090.1_g00001.1

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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC155337	1e-159	AC155337.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH117N09, complete sequence.
GenBank	AC189220	1e-159	AC189220.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB010H06, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018438257.1	1e-132	PREDICTED: LOB domain-containing protein 16
Swissprot	Q9SLB7	1e-123	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	D7LI59	1e-122	D7LI59_ARALL; Uncharacterized protein
STRING	Bostr.25993s0538.1.p	1e-124	(Boechera stricta)

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	7e-85	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]