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.I00424.1

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: 239aa MW: 25007.7 Da PI: 6.3313

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pahal.I00424.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	127.7	5.2e-40	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+++Cv+apyf++eq +++fa++hk+FGasnv+kll++lp +r++a+ ++ yeA+ar+rdP+yG+v++i++lqqq+++l+a+l Pahal.I00424.1 7 PCGACKFLRRKCVRGCVFAPYFCHEQgAAHFAAIHKVFGASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQAQL 101 7***********************89***************************************************************** PP DUF260 95 allkee 100 a+lk++ Pahal.I00424.1 102 ASLKAQ 107 *99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.574	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	5.9E-38	7	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 239 aa Download sequence Send to blast
MTGFGSPCGA CKFLRRKCVR GCVFAPYFCH EQGAAHFAAI HKVFGASNVS KLLAHLPLAD 60 RPEAAVTISY EAQARLRDPI YGCVAHIFAL QQQVMTLQAQ LASLKAQAAQ GHAGVHEDAK 120 GYMGSAAEQL GYGYPWCGSN GGAGAVGAPP AAQPSAYSNG GHESLTALLG SDYMQQSLYH 180 AFEQAGAADD DGRQAAAFEA AADSSSFGAE ESGWRSSSGY QDCEDLQSVA YAYLNHRS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-35	3	101	7	104	LOB family transfactor Ramosa2.1
5ly0_B	7e-35	3	101	7	104	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}.

Regulation -- Description ? help Back to Top
Source	Description
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	EF051732	0.0	EF051732.1 Zea mays rootless concerning crown and seminal lateral roots (rtcs) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025797613.1	1e-174	LOB domain-containing protein CRL1-like
Swissprot	Q5UG13	1e-115	LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBL	A0A2S3IU95	1e-172	A0A2S3IU95_9POAL; Uncharacterized protein
TrEMBL	A0A2T7CHM3	1e-172	A0A2T7CHM3_9POAL; Uncharacterized protein
STRING	Pavir.Ib00283.1.p	1e-156	(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
AT2G42440.1	1e-56	LBD family protein

Link Out ? help Back to Top
Phytozome	Pahal.I00424.1

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]