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_009138972.1

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: 219aa MW: 24376 Da PI: 6.7859

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009138972.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	122.1	2.9e-38	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkCa++Cv+apyf++eq +++fa++hk+FGasn +k+l++lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+a+l XP_009138972.1 7 PCGACKFLRRKCANGCVFAPYFCHEQgASHFAAIHKVFGASNASKILSNLPISDRCEAAITISYEAQARLHDPIYGCVSHIFALQQQVVNLQAQL 101 7***********************89*************************************************************** PP DUF260 95 allkee 100 + lk++ XP_009138972.1 102 EILKQQ 107 9997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.319	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	4.1E-36	7	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 219 aa Download sequence Send to blast
MSSSGSPCGA CKFLRRKCAN GCVFAPYFCH EQGASHFAAI HKVFGASNAS KILSNLPISD 60 RCEAAITISY EAQARLHDPI YGCVSHIFAL QQQVVNLQAQ LEILKQQVAQ SMMFADSPSS 120 ENPNSYYGDN TKTSYHHDHH QEHRNIHHHH HDETRLVYQT GSSGMVQHGD ATVNSYPTGN 180 CSGFGEVFIY PDLEQHLNSF NQDHLKELQS ANFGYISFS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-33	4	102	8	105	LOB family transfactor Ramosa2.1
5ly0_B	1e-33	4	102	8	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_009138972.1

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_009138972.1	1e-164	PREDICTED: LOB domain-containing protein 29
Swissprot	Q9M2J7	1e-129	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	M4DDL3	1e-162	M4DDL3_BRARP; Uncharacterized protein
STRING	Bra014581.1-P	1e-163	(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-113	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]