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

Lj0g3v0342589.2

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: 958aa MW: 106317 Da PI: 5.6162

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj0g3v0342589.2	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.8	2e-23	184	285	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+ +++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++gD+v+F +++ Lj0g3v0342589.2 184 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldyTIQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSVLFI--RDE 274 99*******************99998555555.59********************************************..456 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 +l+v+v+r+ Lj0g3v0342589.2 275 ISQLRVGVRRA 285 7777**997 PP
2	Auxin_resp	115.6	4.4e-38	310	393	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++ka++ +++svGmRf m+fete+s +rr++Gt+vg++d+dp+rWp+SkWr+++ Lj0g3v0342589.2 310 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYRKAVYaSQLSVGMRFGMMFETEESGKRRYMGTIVGINDVDPLRWPGSKWRNIQ 393 79*******************************989*****************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	7.06E-46	173	313	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.1E-40	176	298	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.54E-22	183	284	No hit	No description
Pfam	PF02362	8.5E-21	184	285	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.788	184	286	IPR003340	B3 DNA binding domain
SMART	SM01019	4.1E-23	184	286	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.5E-33	310	393	IPR010525	Auxin response factor
Pfam	PF02309	4.8E-11	849	939	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	23.746	852	936	IPR000270	PB1 domain
SuperFamily	SSF54277	5.98E-8	865	931	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009733	Biological Process	response to auxin
GO:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 958 aa Download sequence Send to blast
MASVEEKIKT GGVGVGVGVG VVGGQTQTQN LVAEMKLLKD CGLFPFFVCI EETKINLLLW 60 FFTCLFMLLI FSGVRRTLNS ELWHACAGPL VSLPQVGSLV YYFPQGHSEQ VAASTRRTAT 120 SQIPNYPSLQ SQLLCQVQNV TLHADKETDE IYAQMSLQPV NSEKEVFPIS DFGTKQSKHP 180 SEFFCKTLTA SDTSTHGGFS VPRRAAEKLF PQLDYTIQPP TQELVVRDLH DNTWTFRHIY 240 RGQPKRHLLT TGWSLFVGSK RLRAGDSVLF IRDEISQLRV GVRRANRQQT TLPSSVLSAD 300 SMHIGVLAAA AHAAANRSPF TIFYNPRACP SEFVIPLAKY RKAVYASQLS VGMRFGMMFE 360 TEESGKRRYM GTIVGINDVD PLRWPGSKWR NIQVEWDEPG CGDKQNRVSV WDIETPESLF 420 IFPSLTSSLK RPLQSGLLEN EWGTLLRKPF IKAPESGAME LSSSIPNLYQ EQLMKMLFKP 480 QAVNNNGAFP SLMQQESAAT RGPLQVDNQN VHLASTGSMT LKNPCSQSSQ NSQTTLLKSD 540 QPEKLHPQPR IDNHLTSGTV TDNKSRLESE VLDHVLDFPS MEGCKIEKMV TNPINPQNLA 600 SHLTINNQNQ NPLLPQSSTW PMQHTQLESS LSYPQVIDMS QSDSAIVNGT LPQLDIEEWM 660 AYSSCQPFAG QNRSNGPFSD FQEHASLQAQ VVNNPSLTST NQEVLDHYVK NLKFFSQADQ 720 LTSIYGFNGI SSSNNLRDLS SESNNQSEIC VNVDVSNSVN TTTVDPSTTS STILDEFCTM 780 KERDFQHPQE CMVGNLSCSQ DGQSQITSAS LAESHAFCLR DNSGGTSSSH VDFDDSSLLQ 840 NNSWQQGSTP IRTYTKVQKA GSVGRSIDVT TFKNYEELIR AIECMFGLDG LLNDTKGSGW 900 KLVYVDYESD VLLVGDDPWE EFVGCVRCIR ILSPSEVQQM SEEGMKLLNS GALQGINV

Sequence ? help Back to Top

Protein Sequence Length: 958 aa Download sequence Send to blast

MASVEEKIKT GGVGVGVGVG VVGGQTQTQN LVAEMKLLKD CGLFPFFVCI EETKINLLLW  60
FFTCLFMLLI FSGVRRTLNS ELWHACAGPL VSLPQVGSLV YYFPQGHSEQ VAASTRRTAT  120
SQIPNYPSLQ SQLLCQVQNV TLHADKETDE IYAQMSLQPV NSEKEVFPIS DFGTKQSKHP  180
SEFFCKTLTA SDTSTHGGFS VPRRAAEKLF PQLDYTIQPP TQELVVRDLH DNTWTFRHIY  240
RGQPKRHLLT TGWSLFVGSK RLRAGDSVLF IRDEISQLRV GVRRANRQQT TLPSSVLSAD  300
SMHIGVLAAA AHAAANRSPF TIFYNPRACP SEFVIPLAKY RKAVYASQLS VGMRFGMMFE  360
TEESGKRRYM GTIVGINDVD PLRWPGSKWR NIQVEWDEPG CGDKQNRVSV WDIETPESLF  420
IFPSLTSSLK RPLQSGLLEN EWGTLLRKPF IKAPESGAME LSSSIPNLYQ EQLMKMLFKP  480
QAVNNNGAFP SLMQQESAAT RGPLQVDNQN VHLASTGSMT LKNPCSQSSQ NSQTTLLKSD  540
QPEKLHPQPR IDNHLTSGTV TDNKSRLESE VLDHVLDFPS MEGCKIEKMV TNPINPQNLA  600
SHLTINNQNQ NPLLPQSSTW PMQHTQLESS LSYPQVIDMS QSDSAIVNGT LPQLDIEEWM  660
AYSSCQPFAG QNRSNGPFSD FQEHASLQAQ VVNNPSLTST NQEVLDHYVK NLKFFSQADQ  720
LTSIYGFNGI SSSNNLRDLS SESNNQSEIC VNVDVSNSVN TTTVDPSTTS STILDEFCTM  780
KERDFQHPQE CMVGNLSCSQ DGQSQITSAS LAESHAFCLR DNSGGTSSSH VDFDDSSLLQ  840
NNSWQQGSTP IRTYTKVQKA GSVGRSIDVT TFKNYEELIR AIECMFGLDG LLNDTKGSGW  900
KLVYVDYESD VLLVGDDPWE EFVGCVRCIR ILSPSEVQQM SEEGMKLLNS GALQGINV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	418	5	392	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Lja.20685	0.0	pod

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: In early embryo and during organ development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant with a lower expression in leaves. Detected in embryo axis, provascular tissues, procambium and some differentiated vascular regions of mature organs. {ECO:0000269\|PubMed:10476078}.

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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj0g3v0342589.2

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027331369.1	0.0	auxin response factor 5-like isoform X1
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A445H8Z3	0.0	A0A445H8Z3_GLYSO; Auxin response factor
STRING	GLYMA14G40540.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8991	32	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]