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

Lj6g3v1174050.1

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 304aa MW: 33869.6 Da PI: 8.1118

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj6g3v1174050.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.5	5.3e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ ++W++++iyr++++r++lt+GW+ F + ++L +gD+v+F ++ Lj6g3v1174050.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDNTWTFRHIYRGQPKRHLLTTGWSVFISTKRLFAGDSVLFV--RD 215 99***************************954.4444.48**********************************************..55 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 ++++l++++ r+ Lj6g3v1174050.1 216 EKQQLLLGIKRA 227 788889998775 PP
2	Auxin_resp	75.1	1.9e-25	252	304	1	53
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafeted 53 aahaas++s+F+++YnPr+s+seFv++++k++k+++++vs+GmRf+m+fete+ Lj6g3v1174050.1 252 AAHAASNNSPFTIFYNPRTSPSEFVIPLAKYNKSMYSQVSLGMRFRMMFETEE 304 79*************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.49E-45	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.1E-41	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.17E-20	125	217	No hit	No description
PROSITE profile	PS50863	12.026	126	228	IPR003340	B3 DNA binding domain
SMART	SM01019	9.0E-23	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.1E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.7E-20	252	304	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 304 aa Download sequence Send to blast
MKAPPNGYLP NSGEGERKSI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 ADFIPSYPNL PSKLICMLHN VALHADPETD EVYAQMTLQP VNKYDKEAML ASDMGLKQNN 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDNTWTFRH 180 IYRGQPKRHL LTTGWSVFIS TKRLFAGDSV LFVRDEKQQL LLGIKRANRQ QTALSSSVIS 240 SDSMHIGILA AAAHAASNNS PFTIFYNPRT SPSEFVIPLA KYNKSMYSQV SLGMRFRMMF 300 ETEE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-150	15	304	45	337	Auxin response factor 5
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj6g3v1174050.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003533798.1	0.0	auxin response factor 19
Refseq	XP_020205510.1	0.0	auxin response factor 19
Refseq	XP_028180693.1	0.0	auxin response factor 19-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A151R1N3	0.0	A0A151R1N3_CAJCA; Auxin response factor
TrEMBL	A0A445IY81	0.0	A0A445IY81_GLYSO; Auxin response factor
STRING	GLYMA09G08350.1	0.0	(Glycine max)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	1e-173	auxin response factor 19

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] Wójcikowska B,Gaj MD Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep., 2017. 36(6): p. 843-858 [PMID:28255787] 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] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290]