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

Lj0g3v0282089.1

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: 633aa MW: 69356.9 Da PI: 7.2109

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj0g3v0282089.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	78	1e-24	45	146	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + + Lj0g3v0282089.1 45 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGLEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGD 135 99**************************963.3445679********************************************..348 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 ++el+++++r+ Lj0g3v0282089.1 136 DGELRLGIRRA 146 9999**996 PP
2	Auxin_resp	118.9	4.1e-39	171	252	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +a+a+s++++F+ +YnPr+s+seF+++v+k++k+l++++svGmRf+m+feteds+err++G+v g+sd+dpvrWp+SkWr+L Lj0g3v0282089.1 171 VANALSSRCAFSACYNPRVSSSEFIIPVNKFMKSLDCSYSVGMRFRMRFETEDSAERRFTGLVLGISDVDPVRWPGSKWRCL 252 689******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	6.67E-43	38	151	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.6E-40	39	148	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.26E-22	43	145	No hit	No description
SMART	SM01019	2.0E-23	45	147	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.437	45	147	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.1E-23	45	146	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.6E-33	171	252	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:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 633 aa Download sequence Send to blast
MSPDTMLENL SIYDQVEKNL GEGDTDADGE EDTEAMVKST TPHMFCKTLT ASDTSTHGGF 60 SVPRRAAEDC FPPLDYSQQR PSQELVAKDL HGLEWKFRHI YRGQPRRHLL TTGWSAFVNK 120 KKLVSGDAVL FLRGDDGELR LGIRRAAQLK SVGSFAAPSG QHLSPGTLMD VANALSSRCA 180 FSACYNPRVS SSEFIIPVNK FMKSLDCSYS VGMRFRMRFE TEDSAERRFT GLVLGISDVD 240 PVRWPGSKWR CLLVRWDDIE AGRHNRVSPW EIEPFGSASN NLMAAGLKRT RIGMTSTKME 300 FPAPNGIGTS DFGESLRFQK VLQGQEIMGV NTPFDGINAQ SPRFYELGRC YPGSNCSGIA 360 TTGNSMRVPQ VTSDFSCNGT GFSESFRFPK VLQGQEILPS PPYGALSVDE ARGYGRFGRF 420 DGYQPLSSRN GWPAQMHDNT SHLHTSVTSG QVSSPSSVLM FQQAINPVSN RDYNMEREGK 480 VHYQGSYASE VKGGAFAPSL SDNPILSGRA GVFSNFHSQL GSSRLHDSVS AMRSSQELVP 540 SCKSGCRLFG FSLTEDTHIA NEETEASNSG PSFTRLVEDE FHPGLSLRSK GVGSNCTKPI 600 PLIPPFFPAT DIGGASMSPM QATPLMVIRH MQG

Sequence ? help Back to Top

Protein Sequence Length: 633 aa Download sequence Send to blast

MSPDTMLENL SIYDQVEKNL GEGDTDADGE EDTEAMVKST TPHMFCKTLT ASDTSTHGGF  60
SVPRRAAEDC FPPLDYSQQR PSQELVAKDL HGLEWKFRHI YRGQPRRHLL TTGWSAFVNK  120
KKLVSGDAVL FLRGDDGELR LGIRRAAQLK SVGSFAAPSG QHLSPGTLMD VANALSSRCA  180
FSACYNPRVS SSEFIIPVNK FMKSLDCSYS VGMRFRMRFE TEDSAERRFT GLVLGISDVD  240
PVRWPGSKWR CLLVRWDDIE AGRHNRVSPW EIEPFGSASN NLMAAGLKRT RIGMTSTKME  300
FPAPNGIGTS DFGESLRFQK VLQGQEIMGV NTPFDGINAQ SPRFYELGRC YPGSNCSGIA  360
TTGNSMRVPQ VTSDFSCNGT GFSESFRFPK VLQGQEILPS PPYGALSVDE ARGYGRFGRF  420
DGYQPLSSRN GWPAQMHDNT SHLHTSVTSG QVSSPSSVLM FQQAINPVSN RDYNMEREGK  480
VHYQGSYASE VKGGAFAPSL SDNPILSGRA GVFSNFHSQL GSSRLHDSVS AMRSSQELVP  540
SCKSGCRLFG FSLTEDTHIA NEETEASNSG PSFTRLVEDE FHPGLSLRSK GVGSNCTKPI  600
PLIPPFFPAT DIGGASMSPM QATPLMVIRH MQG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	6e-86	41	282	120	362	Auxin response factor 1
4ldw_A	6e-86	41	282	120	362	Auxin response factor 1
4ldw_B	6e-86	41	282	120	362	Auxin response factor 1
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected during gynoecium development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078, ECO:0000269\|PubMed:9409666}.

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 the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj0g3v0282089.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

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	FJ617270	0.0	FJ617270.1 Lotus japonicus auxin response factor 3b (ARF3b) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027361886.1	0.0	auxin response factor 3-like isoform X1
Swissprot	O23661	1e-150	ARFC_ARATH; Auxin response factor 3
TrEMBL	D3GBU7	0.0	D3GBU7_LOTJA; Auxin response factor
STRING	GLYMA13G30750.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4576	33	55

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-145	ARF family protein

Publications ? help Back to Top
Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] 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] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]