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

RrC2837_p3

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: 150aa MW: 16315.9 Da PI: 6.4232

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC2837_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	68.4	1.6e-21	11	79	32	100
DUF260 32 nvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallkee 100 +hk+FGasn +k+l++lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+ +l+ lk++ RrC2837_p3 11 SIHKVFGASNASKILSNLPISDRCEAAITISYEAQARLQDPIYGCVSHIFALQQQVVNLQGQLEILKQQ 79 69**************************************************************99997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	12.196	1	80	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	5.4E-20	10	77	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 150 aa Download sequence Send to blast
MSSSGSPCGA SIHKVFGASN ASKILSNLPI SDRCEAAITI SYEAQARLQD PIYGCVSHIF 60 ALQQQVVNLQ GQLEILKQQA AQSIMFADSP SSENPSSYYG DNTTTPYHHQ EHQNIHHHHH 120 DQTHLVNQTG SSGMVQRGDA IANSYPTENS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	5e-17	10	74	41	105	LOB family transfactor Ramosa2.1
5ly0_B	5e-17	10	74	41	105	LOB family transfactor Ramosa2.1
Search in ModeBase

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	1e-127	AB473849.1 Arabidopsis thaliana ASL16 mRNA for ASYMMETRIC LEAVES2-like 16 protein, complete cds.
GenBank	AF447893	1e-127	AF447893.1 Arabidopsis thaliana LOB DOMAIN 29 (LBD29) mRNA, complete cds.
GenBank	BT025282	1e-127	BT025282.1 Arabidopsis thaliana At3g58190 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018461781.1	2e-82	PREDICTED: LOB domain-containing protein 29-like
Swissprot	Q9M2J7	2e-77	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A397ZNS0	5e-79	A0A397ZNS0_BRACM; Uncharacterized protein
STRING	Bra014581.1-P	7e-79	(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	4e-59	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]