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

Carubv10001875m

Common Name

CARUB_v10001875mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 232aa MW: 24125.4 Da PI: 7.2029

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10001875m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	130.3	8e-41	19	119	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++pe++r+da+ s+++eA+ar+rdP+yG+v++i +lqqq+ +l++e Carubv10001875m 19 PCGACKFLRRKCVAGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHVPEHKRPDAVVSICFEAQARLRDPIYGCVSHIVSLQQQVLSLQTE 112 7*********************9989************************************************************** PP DUF260 94 lallkee 100 l++l+++ Carubv10001875m 113 LSYLQAH 119 99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.471	18	120	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	3.5E-39	19	117	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: 232 aa Download sequence Send to blast
MSGSGINPSS SGGGGGGGPC GACKFLRRKC VAGCIFAPYF DSEQGAAHFA AVHKVFGASN 60 VSKLLLHVPE HKRPDAVVSI CFEAQARLRD PIYGCVSHIV SLQQQVLSLQ TELSYLQAHL 120 ATLELPQPQP PAVPVSSSGS PLQALSITDL PTISPSVYDL SSIFEPVMSS TWAMQQQPRP 180 SDHLFGLPSS SSIGGGGDLQ ALAREFIHGG QMPSQPSPGT SGSASTMIKR E*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	5e-38	15	120	7	111	LOB family transfactor Ramosa2.1
5ly0_B	5e-38	15	120	7	111	LOB family transfactor Ramosa2.1
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10001875m

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	AB473852	0.0	AB473852.1 Arabidopsis thaliana ASL19 mRNA for ASYMMETRIC LEAVES2-like 19 protein, complete cds.
GenBank	AF432232	0.0	AF432232.1 Arabidopsis thaliana LOB DOMAIN 30 (LBD30) mRNA, complete cds.
GenBank	BT026407	0.0	BT026407.1 Arabidopsis thaliana At4g00220 mRNA, complete cds.
GenBank	DQ446787	0.0	DQ446787.1 Arabidopsis thaliana clone pENTR221-At4g00220 LOB domain protein 30/lateral organ boundaries domain protein 30 (At4g00220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006288584.1	1e-166	LOB domain-containing protein 30
Swissprot	O81323	1e-132	LBD30_ARATH; LOB domain-containing protein 30
TrEMBL	R0FGQ6	1e-165	R0FGQ6_9BRAS; Uncharacterized protein
STRING	Cagra.1261s0014.1.p	1e-166	(Capsella grandiflora)
STRING	XP_006288584.1	1e-166	(Capsella rubella)

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-111	LBD family protein

Link Out ? help Back to Top
Phytozome	Carubv10001875m
Entrez Gene	17881661

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]