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

Cucsa.362840.1

Common Name

Csa_6G076840, LOC101220603

Organism

Cucumis sativus

Taxonomic ID

3659

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

LBD

Protein Properties

Length: 241aa MW: 24752.1 Da PI: 7.5021

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.362840.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	129.6	1.3e-40	29	129	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +l+ael Cucsa.362840.1 29 PCGACKFLRRKCVPGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHIPVHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVSLQAEL 123 7*********************9989***************************************************************** PP DUF260 95 allkee 100 +l+++ Cucsa.362840.1 124 TYLQAH 129 *99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.914	28	130	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.1E-39	29	127	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 241 aa Download sequence Send to blast
MSANPSTSGG GGPGTASTGG SVGAGGGGPC GACKFLRRKC VPGCIFAPYF DSEQGAAHFA 60 AVHKVFGASN VSKLLLHIPV HKRLDAVVTI CYEAQARLRD PVYGCVAHIF ALQQQVVSLQ 120 AELTYLQAHL ATLELPSPPN PPPPPPPPSF PAQPPLSISD LPSASSLPAT YDLSSLFDPM 180 AQPAWAMQQQ RLDHRQFAGG GGGSSTAPGE GDLQALAREL LLRHGAPPCS DASSPQSLSK 240 *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	3e-38	25	123	7	104	LOB family transfactor Ramosa2.1
5ly0_B	3e-38	25	123	7	104	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 (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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00314	DAP	Transfer from AT2G45420	Download

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	LN684337	0.0	LN684337.1 Cucumis melo genomic scaffold, unassembled_sequence31840.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004145058.1	1e-172	PREDICTED: LOB domain-containing protein 18-like
Swissprot	O22131	6e-81	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A0A0KEN5	1e-171	A0A0A0KEN5_CUCSA; Uncharacterized protein
STRING	XP_004145058.1	1e-172	(Cucumis sativus)
STRING	XP_004153747.1	1e-172	(Cucumis sativus)
STRING	XP_004170755.1	1e-172	(Cucumis sativus)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1771	34	93

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45420.1	1e-76	LOB domain-containing protein 18

Link Out ? help Back to Top
Phytozome	Cucsa.362840.1
Entrez Gene	101220603

Publications ? help Back to Top
Ren Y, et al. An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE, 2009. 4(6): p. e5795 [PMID:19495411] Guo S, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384 [PMID:20565788] Li Z, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12: p. 540 [PMID:22047402] 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]