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

OBART08G23860.1

Organism

Oryza barthii

Taxonomic ID

65489

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

LBD

Protein Properties

Length: 215aa MW: 23239.2 Da PI: 6.2822

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OBART08G23860.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	122	3.2e-38	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 +C aCk+lrrkC+k+Cv+apyf++eq +++fa++hk+FGasn +k+l +lp ++r +a+ ++ yeA+ar+rdP+yG+v++i++lqqq+ +l+a+ OBART08G23860.1 7 PCGACKFLRRKCVKGCVFAPYFCHEQgAAHFAAIHKVFGASNASKILMHLPVSDRCEAAVTMSYEAQARLRDPIYGCVAHIFSLQQQVVSLQAQ 100 7***********************89************************************************************** PP DUF260 94 lallkee 100 l++lk++ OBART08G23860.1 101 LESLKAQ 107 99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.695	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.9E-36	7	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 215 aa Download sequence Send to blast
MTGLGSPCGA CKFLRRKCVK GCVFAPYFCH EQGAAHFAAI HKVFGASNAS KILMHLPVSD 60 RCEAAVTMSY EAQARLRDPI YGCVAHIFSL QQQVVSLQAQ LESLKAQATQ GYGDGCSISS 120 PQNDSCGNML TSIVQDEQQF VGPTMASNSS VKNENHSYIA NGHLAPMSAQ SSQGFEAELC 180 MAEYSNTNPC CSVQGNWYHD MEDLQSVAFA YLNQA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-34	3	103	7	106	LOB family transfactor Ramosa2.1
5ly0_B	1e-34	3	103	7	106	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}.

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	AP004587	0.0	AP004587.3 Oryza sativa Japonica Group genomic DNA, chromosome 8, PAC clone:P0543D10.
GenBank	AP014964	0.0	AP014964.1 Oryza sativa Japonica Group DNA, chromosome 8, cultivar: Nipponbare, complete sequence.
GenBank	CP012616	0.0	CP012616.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 8 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015648252.1	1e-161	LOB domain-containing protein CRL1-like
Swissprot	Q5UG13	1e-66	LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBL	A0A0D3H3A5	1e-159	A0A0D3H3A5_9ORYZ; Uncharacterized protein
TrEMBL	A0A0E0AZ21	1e-159	A0A0E0AZ21_9ORYZ; Uncharacterized protein
TrEMBL	A0A0E0IGE8	1e-159	A0A0E0IGE8_ORYNI; Uncharacterized protein
TrEMBL	A0A0E0QMG8	1e-159	A0A0E0QMG8_ORYRU; Uncharacterized protein
TrEMBL	A2YY71	1e-159	A2YY71_ORYSI; Uncharacterized protein
TrEMBL	I1QKH3	1e-159	I1QKH3_ORYGL; Uncharacterized protein
TrEMBL	Q6ZBW8	1e-159	Q6ZBW8_ORYSJ; Os08g0563400 protein
STRING	OGLUM08G25340.1	1e-160	(Oryza glumipatula)
STRING	ORUFI08G26340.1	1e-160	(Oryza rufipogon)
STRING	OS08T0563400-00	1e-160	(Oryza sativa)
STRING	ONIVA09G01330.1	1e-160	(Oryza nivara)
STRING	ORGLA08G0192400.1	1e-160	(Oryza glaberrima)
STRING	OBART08G23860.1	1e-160	(Oryza barthii)

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-54	lateral organ boundaries-domain 29

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]