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_00265.1_g00003.1

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: 216aa MW: 23750.2 Da PI: 6.7848

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00265.1_g00003.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	123.8	8.9e-39	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqq 85 +C aCk+lrrkCa++Cv+apyf++eq +++fa++hk+FGasn +k+l++lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqq Rsa1.0_00265.1_g00003.1 7 PCGACKFLRRKCANGCVFAPYFCHEQgSSHFAAIHKVFGASNASKILSNLPISDRCEAAITISYEAQARLQDPIYGCVSHIFALQQ 92 7***********************88****************************************************** PP DUF260 86 qleqlkaelallkee 100 q+ +l+a+l+ lk++ Rsa1.0_00265.1_g00003.1 93 QVVNLQAQLEILKQQ 107 ********99997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.13	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.9E-36	7	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 216 aa Download sequence Send to blast
MSSSGSPCGA CKFLRRKCAN GCVFAPYFCH EQGSSHFAAI HKVFGASNAS KILSNLPISD 60 RCEAAITISY EAQARLQDPI YGCVSHIFAL QQQVVNLQAQ LEILKQQAAQ SILFADSPSS 120 ENPSSYYGDN TTTPYHHQEH QNIHHHHHDQ THLVNQTGSS GTVQRGDAIA NSYPTENSSG 180 FGQFSIYPDL EQHLNPFNQD HLKVLQSANL GYISFS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	5e-34	4	102	8	105	LOB family transfactor Ramosa2.1
5ly0_B	5e-34	4	102	8	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00265.1_g00003.1

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 -- 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_018461781.1	1e-138	PREDICTED: LOB domain-containing protein 29-like
Swissprot	Q9M2J7	1e-130	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A291LR15	1e-133	A0A291LR15_BRARR; Transcription factor LBD29a
TrEMBL	A0A397ZNS0	1e-132	A0A397ZNS0_BRACM; Uncharacterized protein
STRING	Bra014581.1-P	1e-132	(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]