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.257700.1

Common Name

Csa_3G126090, LOC101216934

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: 232aa MW: 24957.7 Da PI: 8.7511

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.257700.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	124.1	6.9e-39	24	123	1	99
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC ++C++apyf +eq + +fa+vhk+FGasnv+k+l ++pe++r da+ +++yeA+ar+r+Pv G+v++i++lqqq ++l+ e+ Cucsa.257700.1 24 PCGACKFLRRKCMPECIFAPYFDSEQgSTHFAAVHKVFGASNVSKMLLHIPEHKRLDAAITICYEAQARVREPVLGCVSHIFALQQQAARLQIEI 118 7*********************9988***************************************************************** PP DUF260 95 allke 99 ++l++ Cucsa.257700.1 119 SYLQA 123 99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.847	23	125	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.3E-37	24	122	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 232 aa Download sequence Send to blast
MSSRRSGGSC TKGKGGGSNG SGGPCGACKF LRRKCMPECI FAPYFDSEQG STHFAAVHKV 60 FGASNVSKML LHIPEHKRLD AAITICYEAQ ARVREPVLGC VSHIFALQQQ AARLQIEISY 120 LQAYLATSEL PRSAPHLQAQ PPALVKKPTL SSIISLPSDC PSFPAESDLS LLLDPVEQVS 180 QEKLQSPLES YQIGSNNFPS MGSIDQQVVQ KQLSSMQRIG ASLFPNIPKR A*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	6e-36	20	119	7	105	LOB family transfactor Ramosa2.1
5ly0_B	6e-36	20	119	7	105	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}.

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	LN681848	1e-171	LN681848.1 Cucumis melo genomic scaffold, anchoredscaffold00006.
GenBank	LN713260	1e-171	LN713260.1 Cucumis melo genomic chromosome, chr_6.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004134346.1	1e-169	PREDICTED: LOB domain-containing protein 18
Swissprot	O22131	7e-56	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A0A0L4D4	1e-168	A0A0A0L4D4_CUCSA; Uncharacterized protein
STRING	XP_004134346.1	1e-169	(Cucumis sativus)
STRING	XP_004155866.1	1e-168	(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	2e-58	LOB domain-containing protein 18

Link Out ? help Back to Top
Phytozome	Cucsa.257700.1
Entrez Gene	101216934

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]