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

XP_009116510.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 225aa MW: 24753.2 Da PI: 6.498

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009116510.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	117.9	5.9e-37	13	113	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aC++ rr C+k+Cv+apyf++eq +++fa++hk+FGasn +kll++lp+++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+a+l XP_009116510.1 13 PCGACQFPRRPCSKGCVFAPYFCHEQgASHFAAIHKVFGASNASKLLSQLPTSDRCEAAITISYEAQARLQDPIYGCVSHIFALQQQVVNLQAQL 107 7***********************89*************************************************************** PP DUF260 95 allkee 100 + lk++ XP_009116510.1 108 EILKQQ 113 9997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.563	12	114	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.8E-34	13	111	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: 225 aa Download sequence Send to blast
MSSSSSSSLS GSPCGACQFP RRPCSKGCVF APYFCHEQGA SHFAAIHKVF GASNASKLLS 60 QLPTSDRCEA AITISYEAQA RLQDPIYGCV SHIFALQQQV VNLQAQLEIL KQQVAQSMMF 120 ADSPSSENPN SFYGDTTKTT SYHHDHHQEH QNIYHHHDQT HLVNQIGSLG TGQHGDATVN 180 SYPSQNSSGL GEFSIYPELE QHLNTFNQDH LKELQSANFG YISFS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-32	3	108	1	105	LOB family transfactor Ramosa2.1
5ly0_B	7e-32	3	108	1	105	LOB family transfactor Ramosa2.1
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots. {ECO:0000269\|PubMed:12068116}.

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	XP_009116510.1

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_009116510.1	1e-166	PREDICTED: LOB domain-containing protein 29-like
Swissprot	Q9M2J7	1e-131	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	M4CT43	1e-165	M4CT43_BRARP; Uncharacterized protein
STRING	Bra007385.1-P	1e-166	(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
AT3G58190.1	1e-110	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]