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

Spipo22G0039400

Organism

Spirodela polyrhiza

Taxonomic ID

29656

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Araceae; Lemnoideae; Spirodela

Family

LBD

Protein Properties

Length: 217aa MW: 23795.8 Da PI: 5.5745

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Spipo22G0039400	genome	MIPS/IBIS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.8	2.4e-40	9	109	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 +C aCk+lrrkCa++Cv+apyf +q + +fa+vhk+FGasnv+kll++lp ++r++a+ ++ yeA+ar+rdPvyG+v++i++lqqq+++l++e Spipo22G0039400 9 SCGACKFLRRKCAEGCVFAPYFSYDQgAIHFAAVHKVFGASNVSKLLSHLPVQHRSEAAVTISYEAQARMRDPVYGCVSHIFALQQQVASLQEE 102 6***********************889*************************************************************** PP DUF260 94 lallkee 100 +++l ++ Spipo22G0039400 103 IESLTKQ 109 *998877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.235	8	110	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.4E-38	9	106	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 217 aa Download sequence Send to blast
MNMAGLASSC GACKFLRRKC AEGCVFAPYF SYDQGAIHFA AVHKVFGASN VSKLLSHLPV 60 QHRSEAAVTI SYEAQARMRD PVYGCVSHIF ALQQQVASLQ EEIESLTKQL AQTTGDDRNP 120 SPLASDSIWD CFQVCMQVDE FSNQHTGNAS TLSSFSGESK VQGLPAVYKD AIERLEYTLF 180 SDFTNEPSSW EDLSVDMLGD FASCKKGLFT RIVFCK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	9e-36	5	110	7	111	LOB family transfactor Ramosa2.1
5ly0_B	9e-36	5	110	7	111	LOB family transfactor Ramosa2.1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Acts as positive regulator of adventitious (crown) root formation by promoting its initiation (PubMed:15829602, PubMed:15960615). Acts as positive regulator of lateral root formation. Regulated by the auxin response factor and transcriptional activator ARF23/ARF1 (PubMed:15829602). Involved in auxin-mediated cell dedifferentiation, and may promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder at the base of the stem (PubMed:15960615). May act upstream of the gene regulatory network controlling adventitious root (crown) development (PubMed:21806801). {ECO:0000269\|PubMed:15829602, ECO:0000269\|PubMed:15960615, ECO:0000269\|PubMed:21806801}.
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}.
UniProt	INDUCTION: Induced by auxin (PubMed:15829602, PubMed:15960615). Induced by ethylene (PubMed:15960615). {ECO:0000269\|PubMed:15829602, ECO:0000269\|PubMed:15960615}.

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_008372823.1	5e-61	LOB domain-containing protein 33
Swissprot	Q5UG13	4e-54	LBD_ORYSJ; LOB domain-containing protein CRL1
Swissprot	Q9M2J7	1e-54	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A0K9NKR4	9e-60	A0A0K9NKR4_ZOSMR; Putative LOB domain-containing protein
TrEMBL	A0A498JF69	1e-59	A0A498JF69_MALDO; Uncharacterized protein
STRING	XP_008372823.1	2e-60	(Malus domestica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP2501	38	93

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	5e-57	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	Spipo22G0039400

Publications ? help Back to Top
Coudert Y,Périn C,Courtois B,Khong NG,Gantet P Genetic control of root development in rice, the model cereal. Trends Plant Sci., 2010. 15(4): p. 219-26 [PMID:20153971] Kitomi Y, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J., 2011. 67(3): p. 472-84 [PMID:21481033] Coudert Y, et al. Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice. BMC Genomics, 2011. 12: p. 387 [PMID:21806801] 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]