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

Zjn_sc00003.1.g12350.1.am.mk

Organism

Zoysia japonica

Taxonomic ID

309978

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Zoysieae; Zoysiinae; Zoysia

Family

LBD

Protein Properties

Length: 198aa MW: 20632.3 Da PI: 7.3094

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zjn_sc00003.1.g12350.1.am.mk	genome	ZGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	115.6	3e-36	13	102	1	89
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvi 80 +C aCk+lrrkCa++Cv+ap+f+ae+ +++fa++hk+FGasn kll+++ + +r++a+++++yeA+ar+rdPvyG+v++i Zjn_sc00003.1.g12350.1.am.mk 13 PCGACKFLRRKCAAECVFAPHFCAEDgTAQFAAIHKVFGASNAAKLLQQVAPGDRSEAAATVTYEAQARLRDPVYGCVAHI 93 7*********************9989************************************************* PP DUF260 81 lklqqqleq 89 ++lqqq+ + Zjn_sc00003.1.g12350.1.am.mk 94 FALQQQVIS 102 ****865 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.233	12	113	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.6E-35	13	101	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 198 aa Download sequence Send to blast
MASSAGGGAP GSPCGACKFL RRKCAAECVF APHFCAEDGT AQFAAIHKVF GASNAAKLLQ 60 QVAPGDRSEA AATVTYEAQA RLRDPVYGCV AHIFALQQQV ISNTRLYLKV HSLGLLAAPP 120 AVATLQVQVL QAKAQVAQTV ATAGAQAAGS PLLQRWQMEP ESLSTQSSGC YSAPSGDGSA 180 SMQEMYCFGE QEEGSYTR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	2e-31	11	100	9	97	LOB family transfactor Ramosa2.1
5ly0_B	2e-31	11	100	9	97	LOB family transfactor Ramosa2.1
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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}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:23749813}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	FP098210	1e-118	FP098210.1 Phyllostachys edulis cDNA clone: bphyst030e16, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004985693.1	4e-99	LOB domain-containing protein 16
Swissprot	Q9SLB7	5e-47	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A1E5WDM2	1e-99	A0A1E5WDM2_9POAL; LOB domain-containing protein 29
STRING	Si037727m	1e-98	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10262	33	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	2e-41	lateral organ boundaries-domain 29

Publications ? help Back to Top
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]