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_01675.1_g00006.1

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: 222aa MW: 24381.9 Da PI: 6.783

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01675.1_g00006.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	124.3	6.2e-39	11	111	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqq 85 +C aCk+lrrkCak+Cv+apyf++eq +++fa++hk+FGasn +kll++lp+++r +a+ ++ yeA+ar++dP+yG+v++i++lqq Rsa1.0_01675.1_g00006.1 11 PCGACKFLRRKCAKGCVFAPYFCHEQgASHFAAIHKVFGASNASKLLSQLPTSDRCEAAITISYEAQARLQDPIYGCVSHIFALQQ 96 7***********************89****************************************************** PP DUF260 86 qleqlkaelallkee 100 q+ +l+a+l+ lk++ Rsa1.0_01675.1_g00006.1 97 QVVNLQAQLEILKQQ 111 *********9997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.186	10	112	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.2E-36	11	109	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 222 aa Download sequence Send to blast
MSSSSSSSGS PCGACKFLRR KCAKGCVFAP YFCHEQGASH FAAIHKVFGA SNASKLLSQL 60 PTSDRCEAAI TISYEAQARL QDPIYGCVSH IFALQQQVVN LQAQLEILKQ QAAQSMMFAD 120 SPSSGNPSCF HGDTTKTTSY HHDHREHQDI YHHHDQTHLV NQIGSLGTGQ HGNATANSYL 180 SENSSSFGEF SIYPELEQQL NTFNQDHLKE LQSANFGYIS FS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	8e-36	2	106	2	105	LOB family transfactor Ramosa2.1
5ly0_B	8e-36	2	106	2	105	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19. {ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01675.1_g00006.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018490092.1	1e-164	PREDICTED: LOB domain-containing protein 29-like
Swissprot	Q9M2J7	1e-129	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A291LR11	1e-143	A0A291LR11_BRARR; Transcription factor LBD29
TrEMBL	A0A397Y6T0	1e-143	A0A397Y6T0_BRACM; Uncharacterized protein
STRING	Bo8g092560.1	1e-141	(Brassica oleracea)

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
AT3G58190.1	1e-119	lateral organ boundaries-domain 29

Publications ? help Back to Top
Gupta A,Singh M,Laxmi A Interaction between glucose and brassinosteroid during the regulation of lateral root development in Arabidopsis. Plant Physiol., 2015. 168(1): p. 307-20 [PMID:25810094] Porco S, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development, 2016. 143(18): p. 3340-9 [PMID:27578783] 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] Xu C,Cao H,Xu E,Zhang S,Hu Y Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation. Plant Cell Physiol., 2018. 59(4): p. 744-755 [PMID:29121271] 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]