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

RrC79_p5

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: 219aa MW: 23967.5 Da PI: 6.83

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC79_p5	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	124.3	6e-39	11	111	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallkee 100 +C aCk+lrrkCak+Cv+apyf++eq +++fa++hk+FGasn +kll++lp+++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+a+l+ lk++ RrC79_p5 11 PCGACKFLRRKCAKGCVFAPYFCHEQgASHFAAIHKVFGASNASKLLSQLPTSDRCEAAITISYEAQARLQDPIYGCVSHIFALQQQVVNLQAQLEILKQQ 111 7***********************89*******************************************************************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: 219 aa Download sequence Send to blast
MSSSSSSSGS PCGACKFLRR KCAKGCVFAP YFCHEQGASH FAAIHKVFGA SNASKLLSQL 60 PTSDRCEAAI TISYEAQARL QDPIYGCVSH IFALQQQVVN LQAQLEILKQ QAAQSMMFAD 120 SPSSGNPSSF YGDTTKTTSY HHDHQNIYHH RDQTHLVNQI GSLGTGQHGD ATANSYLSEN 180 SSGFGEFSIY PELEQHLNTF NQDHLKELQS ANFGYISFS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-36	2	106	2	105	LOB family transfactor Ramosa2.1
5ly0_B	7e-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}.

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473849	0.0	AB473849.1 Arabidopsis thaliana ASL16 mRNA for ASYMMETRIC LEAVES2-like 16 protein, complete cds.
GenBank	AF447893	0.0	AF447893.1 Arabidopsis thaliana LOB DOMAIN 29 (LBD29) mRNA, complete cds.
GenBank	BT025282	0.0	BT025282.1 Arabidopsis thaliana At3g58190 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013603683.1	1e-148	PREDICTED: LOB domain-containing protein 29
Refseq	XP_013603684.1	1e-148	PREDICTED: LOB domain-containing protein 29
Refseq	XP_013659892.1	1e-148	LOB domain-containing protein 29
Swissprot	Q9M2J7	1e-135	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A0D3DU53	1e-147	A0A0D3DU53_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6FIJ0	1e-146	A0A3P6FIJ0_BRAOL; Uncharacterized protein
STRING	Bo8g092560.1	1e-147	(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-126	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]