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

RrC3356_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

LBD

Protein Properties

Length: 224aa MW: 23679.9 Da PI: 7.1758

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3356_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	132.4	1.8e-41	15	115	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallk 98 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll+++pe++r da+ s+++eA+ar+rdP+yG+v++i +lqqq+ +l++el++++ RrC3356_p2 15 PCGACKFLRRKCVAGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLQHVPEHKRADAVVSICFEAQARLRDPIYGCVSHIVSLQQQVVSLQTELSYVQ 113 7*********************9989*******************************************************************99 PP DUF260 99 ee 100 ++ RrC3356_p2 114 AH 115 86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.65	14	116	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	5.2E-40	15	113	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010199	Biological Process	organ boundary specification between lateral organs and the meristem

Sequence ? help Back to Top
Protein Sequence Length: 224 aa Download sequence Send to blast
MSSSGSPSSS CGGGPCGACK FLRRKCVAGC IFAPYFDSEQ GAAHFAAVHK VFGASNVSKL 60 LQHVPEHKRA DAVVSICFEA QARLRDPIYG CVSHIVSLQQ QVVSLQTELS YVQAHLATLE 120 LPQPPPAPVT SSGSPPPLSI SDLPTITPSL YELSPIFEPM SSTWTMQQQP RPFDHIFGVP 180 SSSTIGGSGE LQALARNFLH GGQIPADQPP QGTCGSAPTV VKRE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	3e-38	5	116	1	111	LOB family transfactor Ramosa2.1
5ly0_B	3e-38	5	116	1	111	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes. {ECO:0000269\|PubMed:19088331}.

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_018454999.1	1e-162	PREDICTED: LOB domain-containing protein 30
Swissprot	O81323	1e-115	LBD30_ARATH; LOB domain-containing protein 30
TrEMBL	A0A397XZA8	1e-142	A0A397XZA8_BRACM; Uncharacterized protein
TrEMBL	M4F8B1	1e-142	M4F8B1_BRARP; Uncharacterized protein
STRING	Bra037323.1-P	1e-143	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G00220.1	1e-102	LBD family protein

Publications ? help Back to Top
Rast-Somssich MI, et al. The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J. Exp. Bot., 2017. 68(11): p. 2741-2755 [PMID:28472464] Liu C,Yu H,Li L SUMO modification of LBD30 by SIZ1 regulates secondary cell wall formation in Arabidopsis thaliana. PLoS Genet., 2019. 15(1): p. e1007928 [PMID:30657769]