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

OBART03G25970.1

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: 119aa MW: 12929.2 Da PI: 6.9976

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OBART03G25970.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	88.1	1.2e-27	7	84	1	75
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeqpkkfanvhklFGasnvlkllkalpeeeredams...slvyeAearardPvyG 75 +CaaCk+lrrkC+++Cv+apyfp +qp+kfanvhk+FGasnv+kll++l++e+reda++ +l y+ e +P +G OBART03G25970.1 7 PCAACKLLRRKCTQGCVFAPYFPPDQPAKFANVHKVFGASNVTKLLNDLQPEQREDATEpamALPYHMEPSPPQPSSG 84 7*****************************************************999762224555555555555555 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	18.013	6	107	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	7.0E-27	7	66	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 119 aa Download sequence Send to blast
MSSSSSPCAA CKLLRRKCTQ GCVFAPYFPP DQPAKFANVH KVFGASNVTK LLNDLQPEQR 60 EDATEPAMAL PYHMEPSPPQ PSSGHSHDEV SQQQHHHHHH RHHHTDGSDE GSGGAAPPG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	3e-31	4	97	8	99	LOB family transfactor Ramosa2.1
5ly0_B	3e-31	4	97	8	99	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Controls the proximal-distal patterning in petals and the adaxial-abaxial determination of leaves. Involved in the repression of the homeobox gene BP. {ECO:0000269\|PubMed:12787254, ECO:0000269\|PubMed:15821980}.
UniProt	Negative regulator of cell proliferation in the adaxial side of leaves. Regulates the formation of a symmetric lamina and the establishment of venation. Positively regulates LATERAL ORGAN BOUNDARIES (LOB) within the shoot apex, and the class III HD-ZIP genes REV, PHB, and PHV. Interacts directly with ASYMMETRIC LEAVES 1 (AS1) to repress the knox homeobox genes KNAT1, KNAT2, and KNAT6 and the abaxial determinants ARF3, KAN2 and YAB5. May act in parallel with the RDR6-SGS3-AGO7 pathway, an endogenous RNA silencing pathway, to regulate the leaf morphogenesis (PubMed:11311158, PubMed:12787254, PubMed:12874130, PubMed:14508003, PubMed:16006579, PubMed:16699177, PubMed:17395603, PubMed:17559509). Required for the binding of AS1 to the KNOX genes (PubMed:23271976). Involved in leaf polarity establishment by functioning cooperatively with RH10 or RID2 to repress abaxial genes ARF3, ARF4, KAN1, KAN2, YAB1 and YAB5, and the knox homeobox genes KNAT1, KNAT2, KNAT6, and STM to promote adaxial development in leaf primordia at shoot apical meristems at high temperatures (PubMed:27334696). {ECO:0000269\|PubMed:11311158, ECO:0000269\|PubMed:12787254, ECO:0000269\|PubMed:12874130, ECO:0000269\|PubMed:14508003, ECO:0000269\|PubMed:16006579, ECO:0000269\|PubMed:16699177, ECO:0000269\|PubMed:17395603, ECO:0000269\|PubMed:17559509, ECO:0000269\|PubMed:23271976, ECO:0000269\|PubMed:27334696}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by SHOOT MERISTEMLESS (STM). {ECO:0000269\|PubMed:11934861}.

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	AC136972	1e-101	AC136972.3 Oryza sativa chromosome 3 BAC OSJNBb0007E22 genomic sequence, complete sequence.
GenBank	AP014959	1e-101	AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.
GenBank	CP012611	1e-101	CP012611.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 3 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015629364.1	8e-36	LOB domain-containing protein 36
Refseq	XP_025879462.1	8e-36	LOB domain-containing protein 36
Swissprot	O04479	2e-31	AS2_ARATH; Protein ASYMMETRIC LEAVES 2
Swissprot	Q9FKZ3	2e-31	LBD36_ARATH; LOB domain-containing protein 36
TrEMBL	A0A0D3FL92	8e-82	A0A0D3FL92_9ORYZ; Uncharacterized protein
STRING	OBART03G25970.1	1e-82	(Oryza barthii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6143	34	56

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G65620.4	5e-34	LBD family protein

Publications ? help Back to Top
Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Mateo-Bonmatí E, et al. Plastid control of abaxial-adaxial patterning. Sci Rep, 2015. 5: p. 15975 [PMID:26522839] Li Z, et al. Transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis. J Integr Plant Biol, 2016. 58(12): p. 959-970 [PMID:27273574] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Kim M,Kim MJ,Pandey S,Kim J Expression and Protein Interaction Analyses Reveal Combinatorial Interactions of LBD Transcription Factors During Arabidopsis Pollen Development. Plant Cell Physiol., 2016. 57(11): p. 2291-2299 [PMID:27519310] Wang Z,Wang Y,Kohalmi SE,Amyot L,Hannoufa A SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2 controls floral organ development and plant fertility by activating ASYMMETRIC LEAVES 2 in Arabidopsis thaliana. Plant Mol. Biol., 2016. 92(6): p. 661-674 [PMID:27605094] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development. G3 (Bethesda), 2018. 8(4): p. 1379-1390 [PMID:29487187]