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

Pahal.F00325.1

Organism

Panicum hallii

Taxonomic ID

206008

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

LBD

Protein Properties

Length: 216aa MW: 23792.7 Da PI: 6.2866

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pahal.F00325.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	120.6	8.8e-38	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+k+Cv+apyf++eq +++fa++hk+FGasn +kll +lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+ael Pahal.F00325.1 7 PCGACKFLRRKCVKGCVFAPYFCHEQgAAHFAAIHKVFGASNASKLLMHLPISDRCEAAVTMSYEAQARLQDPIYGCVAHIFSLQQQVVSLQAEL 101 7***********************89***************************************************************** PP DUF260 95 allkee 100 ++ k++ Pahal.F00325.1 102 ESFKAQ 107 998876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.648	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.2E-35	7	104	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: 216 aa Download sequence Send to blast
MTGLGSPCGA CKFLRRKCVK GCVFAPYFCH EQGAAHFAAI HKVFGASNAS KLLMHLPISD 60 RCEAAVTMSY EAQARLQDPI YGCVAHIFSL QQQVVSLQAE LESFKAQAQG YKDGSLTSNP 120 QKESCERLTP CMQDGQLFFH QTMASNSSVK SESQLYFAND CFNSESAQYS EGYEPDLCMP 180 DYNHSNPSCN MKGIRYHDMN DLQSQSVAST YLNEA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-36	3	120	7	123	LOB family transfactor Ramosa2.1
5ly0_B	4e-36	3	120	7	123	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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JN672670	1e-100	JN672670.1 Eragrostis tef bio-material GRIN PI524434 clone Tefdw3b, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025820157.1	1e-161	LOB domain-containing protein 29-like
Swissprot	Q5UG13	1e-63	LBD_ORYSJ; LOB domain-containing protein CRL1
Swissprot	Q9M2J7	4e-64	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A2S3I4W7	1e-160	A0A2S3I4W7_9POAL; Uncharacterized protein
STRING	Pavir.Fa00011.1.p	1e-140	(Panicum virgatum)

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	2e-66	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	Pahal.F00325.1

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]