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

Medtr7g096530.1

Common Name

MTR_7g096530

Organism

Medicago truncatula

Taxonomic ID

3880

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago

Family

LBD

Protein Properties

Length: 219aa MW: 24173.3 Da PI: 7.4255

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Medtr7g096530.1	genome	Mt	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	129.7	1.3e-40	14	115	1	101
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 +C aCk+lrrkCa+dC++apyf++eq p++fa++hk+FGasnv+kll ++p +er +a+ +++yeA+ar+rdPvyG+v++i++lqqq+++l+a+ Medtr7g096530.1 14 PCGACKFLRRKCAPDCIFAPYFCSEQgPARFAAIHKVFGASNVSKLLLHIPAHERCEAVVTIAYEAQARIRDPVYGCVSHIFALQQQVACLQAQ 107 7***********************99************************************************************** PP DUF260 94 lallkeel 101 l ++k++l Medtr7g096530.1 108 LMQVKSQL 115 999875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.367	13	115	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	6.4E-39	14	112	IPR004883	Lateral organ boundaries, LOB
Gene3D	G3DSA:3.90.249.10	7.6E-4	117	205	IPR016110	Adenovirus Pll, hexon, subdomain 3

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus
GO:0019028	Cellular Component	viral capsid
GO:0005198	Molecular Function	structural molecule activity

Sequence ? help Back to Top
Protein Sequence Length: 219 aa Download sequence Send to blast
MASSNGTSSG TGSPCGACKF LRRKCAPDCI FAPYFCSEQG PARFAAIHKV FGASNVSKLL 60 LHIPAHERCE AVVTIAYEAQ ARIRDPVYGC VSHIFALQQQ VACLQAQLMQ VKSQLSHNIE 120 NNNQWIGNNN NVAATQAMNY PFCPTYMNPI SPQSSLESSI DHSSSMNDGM MSMQDVQSSR 180 EDFSFQGCNN YKKRMPHNNN NDHDLGELQE IAIRMMRN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	3e-40	7	115	4	111	LOB family transfactor Ramosa2.1
5ly0_B	3e-40	7	115	4	111	LOB family transfactor Ramosa2.1
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269\|PubMed:19717544}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots and faintly in shoots. {ECO:0000269\|PubMed:12068116}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:26059335}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00309	DAP	Transfer from AT2G42430	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Medtr7g096530.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263, 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	BT142364	0.0	BT142364.1 Medicago truncatula clone JCVI-FLMt-14N17 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013449860.1	1e-164	LOB domain-containing protein 16
Swissprot	Q9SLB7	5e-77	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A072U455	1e-163	A0A072U455_MEDTR; LOB domain protein
STRING	XP_004493763.1	1e-115	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4509	33	58

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42430.1	9e-53	lateral organ boundaries-domain 16

Link Out ? help Back to Top
Phytozome	Medtr7g096530.1
Entrez Gene	25499227

Publications ? help Back to Top
Young ND, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 2011. 480(7378): p. 520-4 [PMID:22089132] Bargmann BO,Birnbaum KD,Brenner ED An undergraduate study of two transcription factors that promote lateral root formation. Biochem Mol Biol Educ, 2014 May-Jun. 42(3): p. 237-45 [PMID:24615800] Cabrera J,Fenoll C,Escobar C Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis. Plant Signal Behav, 2015. 10(3): p. e990825 [PMID:25664644] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Jeon E, et al. LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis. Plant Cell Physiol., 2017. 58(12): p. 2190-2201 [PMID:29040694] 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] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751] Liu J, et al. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. Plant Cell Physiol., 2018. 59(4): p. 734-743 [PMID:29361138] 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]