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

28428.m000040

Common Name

LOC8261015, RCOM_0245570

Organism

Ricinus communis

Taxonomic ID

3988

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus

Family

LBD

Protein Properties

Length: 225aa MW: 24675.3 Da PI: 6.4051

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
28428.m000040	genome	JCVI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	126.3	1.5e-39	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaela 95 +C aCk+lrrkC+++Cv+apyf++eq + +fa++hk+FGasnv+kll++lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+++l+a+la 28428.m000040 7 PCGACKFLRRKCVRGCVFAPYFCHEQgATHFAAIHKVFGASNVSKLLAHLPVSDRCEAAVTISYEAQARLQDPIYGCVSHIFALQQQVMNLQAQLA 102 7***********************89****************************************************************** PP DUF260 96 llkee 100 +lke+ 28428.m000040 103 SLKEQ 107 99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.243	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	9.9E-38	7	105	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: 225 aa Download sequence Send to blast
MTGSGSPCGA CKFLRRKCVR GCVFAPYFCH EQGATHFAAI HKVFGASNVS KLLAHLPVSD 60 RCEAAVTISY EAQARLQDPI YGCVSHIFAL QQQVMNLQAQ LASLKEQAAQ TLINGSATAN 120 PNDKYYGKPS SLPQDLQSWF QSENSNTIPQ FNPSFTTAGE NGFLDPYSMG SYGSSSTTAT 180 SFDSFEEASS SFDMQTDNKQ WNTSYHHHQD PDDLRSVAFG YIQHS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	9e-36	3	101	7	104	LOB family transfactor Ramosa2.1
5ly0_B	9e-36	3	101	7	104	LOB family transfactor Ramosa2.1
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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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	28428.m000040

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}.

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_025015760.1	1e-170	LOB domain-containing protein 29
Swissprot	Q5UG13	6e-71	LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBL	B9T847	1e-168	B9T847_RICCO; LOB domain-containing protein, putative
STRING	XP_002534416.1	1e-169	(Ricinus communis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF3571	33	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	9e-72	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	28428.m000040
Entrez Gene	8261015

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]