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

Csa04g063340.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 264aa MW: 27185.4 Da PI: 7.7988

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa04g063340.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	127.5	6e-40	38	138	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+++C++apyf +eq + fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l+ae+ Csa04g063340.1 38 PCGACKFLRRKCVPGCIFAPYFDSEQgSGYFAAVHKVFGASNVSKLLLHIPVHRRSDAVVTICYEAQARIRDPIYGCVAHIFALQQQVVNLQAEV 132 7*********************997899*************************************************************** PP DUF260 95 allkee 100 ++l+++ Csa04g063340.1 133 SYLQAH 138 *99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.781	37	139	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	6.7E-39	38	136	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 264 aa Download sequence Send to blast
MSGGGNTITA VGGGGGGCGG GGSSGGGGSS SGSGGGGPCG ACKFLRRKCV PGCIFAPYFD 60 SEQGSGYFAA VHKVFGASNV SKLLLHIPVH RRSDAVVTIC YEAQARIRDP IYGCVAHIFA 120 LQQQVVNLQA EVSYLQAHLA SLELPQPQTR PPPLSQQQQL FFAPAPPFSV TDLPASVSPL 180 PSTYDLASIF DQTTPSSAWA TQQRRFVDPR QQYGVPSSSS SAAAIGLGGE NSDLQALAHE 240 LLHRQGSPPP AATDDSPSRS MSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	6e-39	34	139	7	111	LOB family transfactor Ramosa2.1
5ly0_B	6e-39	34	139	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 (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:23872272, ECO:0000269\|PubMed:26059335}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa04g063340.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:23749813}.

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	AB473853	0.0	AB473853.1 Arabidopsis thaliana ASL20 mRNA for ASYMMETRIC LEAVES2-like 20 protein, complete cds.
GenBank	AF447891	0.0	AF447891.1 Arabidopsis thaliana LOB DOMAIN 18 (LBD18) mRNA, complete cds.
GenBank	BT025716	0.0	BT025716.1 Arabidopsis thaliana At2g45420 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010506484.1	0.0	PREDICTED: LOB domain-containing protein 18
Swissprot	O22131	1e-129	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	V4N211	1e-143	V4N211_EUTSA; Uncharacterized protein
STRING	XP_010506484.1	0.0	(Camelina sativa)

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
AT2G45420.1	1e-116	LOB domain-containing protein 18

Publications ? help Back to Top
Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Lee HW, et al. Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation. Plant Physiol., 2017. 174(1): p. 301-311 [PMID:28336771] Pandey SK,Kim J Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis. Plant Signal Behav, 2018. 13(1): p. e1411450 [PMID:29227192] Pandey SK, et al. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. Plant J., 2018. 95(2): p. 233-251 [PMID:29681137] Lee HW, et al. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC Plant Biol., 2019. 19(1): p. 46 [PMID:30704405]