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

Lj1g3v2155550.1

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: 664aa MW: 73460.4 Da PI: 6.6554

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj1g3v2155550.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.1	1.9e-24	149	250	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+ +++++ +l+++d++ ++W++++iyr++++r++lt+GW++Fv ++L++gD+v+F ++ Lj1g3v2155550.1 149 FCKILTASDTSTHGGFSVPRRAAEKLfppldytAQPPTQ--ELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSSFVGLKRLRAGDSVLFI--RD 238 99*******************999996444444..8********************************************..45 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 ++ +l+v+++r+ Lj1g3v2155550.1 239 EKSQLLVGIRRA 250 77778***97 PP
2	Auxin_resp	113	2.8e-37	275	358	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++ka++ +++svGmRf m+fete+s +rr++Gt+vg+sdldp++Wp+SkW++++ Lj1g3v2155550.1 275 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYRKAVYeTQLSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLKWPGSKWQNIQ 358 79*******************************989****************************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.18E-46	138	278	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.0E-42	143	263	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.27E-22	148	249	No hit	No description
PROSITE profile	PS50863	13.422	149	251	IPR003340	B3 DNA binding domain
Pfam	PF02362	4.2E-22	149	250	IPR003340	B3 DNA binding domain
SMART	SM01019	2.3E-24	149	251	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.9E-32	275	358	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

Sequence ? help Back to Top
Protein Sequence Length: 664 aa Download sequence Send to blast
MVSVEVKTKP LGEGRGHNVG GGSVAAEMNL LKEHCGSRFP KGINPELWHA CAGPLVSLPQ 60 LGSLAYYFPQ GHIEQVAAST LGIVTSQIPN YTNLPSQLLC QVQNVTLHAD KETDEVFAQM 120 SLQPLDSEKD VFPTCDFGIK LSKHPTEFFC KILTASDTST HGGFSVPRRA AEKLFPPLDY 180 TAQPPTQELV VRDLHDNTWT FRHIYRGQPK RHLLTTGWSS FVGLKRLRAG DSVLFIRDEK 240 SQLLVGIRRA NRQQTSLPSS VLSADSMQIG VLAAAAHAAA NRSPFTIFYN PRACPSEFVI 300 PLAKYRKAVY ETQLSVGMRF GMMFETEESG KRRYMGTIVG ISDLDPLKWP GSKWQNIQVE 360 WDEPGCTDKQ KRVSSWDIET PESLFIFQSL ASSLKRPLQS GLLGAENGRN ALVRRPFMPV 420 PENGTVGLLN TMPNLYSEQM IKTLMKPQLV NNTGNCLWVR QQEYAAMRGP LEEVSTIPPT 480 AYHKVHLASS MSTPQVNLHF QPKPDQSNAL NLHSKLKSDE LEKLHPPTKV DNPLSSGTVS 540 DKSKSESEGL SVGIFDFPSF EGCNVEKMAF NPLSPQSLAE QLAFLNQNQT PSAVDIPQSD 600 SHIVNGPLPQ LDMDEWMRDS SETNNLSEIY SSINIDGSNS VSVADPSFTS SAILDECFTL 660 KERK

Sequence ? help Back to Top

Protein Sequence Length: 664 aa Download sequence Send to blast

MVSVEVKTKP LGEGRGHNVG GGSVAAEMNL LKEHCGSRFP KGINPELWHA CAGPLVSLPQ  60
LGSLAYYFPQ GHIEQVAAST LGIVTSQIPN YTNLPSQLLC QVQNVTLHAD KETDEVFAQM  120
SLQPLDSEKD VFPTCDFGIK LSKHPTEFFC KILTASDTST HGGFSVPRRA AEKLFPPLDY  180
TAQPPTQELV VRDLHDNTWT FRHIYRGQPK RHLLTTGWSS FVGLKRLRAG DSVLFIRDEK  240
SQLLVGIRRA NRQQTSLPSS VLSADSMQIG VLAAAAHAAA NRSPFTIFYN PRACPSEFVI  300
PLAKYRKAVY ETQLSVGMRF GMMFETEESG KRRYMGTIVG ISDLDPLKWP GSKWQNIQVE  360
WDEPGCTDKQ KRVSSWDIET PESLFIFQSL ASSLKRPLQS GLLGAENGRN ALVRRPFMPV  420
PENGTVGLLN TMPNLYSEQM IKTLMKPQLV NNTGNCLWVR QQEYAAMRGP LEEVSTIPPT  480
AYHKVHLASS MSTPQVNLHF QPKPDQSNAL NLHSKLKSDE LEKLHPPTKV DNPLSSGTVS  540
DKSKSESEGL SVGIFDFPSF EGCNVEKMAF NPLSPQSLAE QLAFLNQNQT PSAVDIPQSD  600
SHIVNGPLPQ LDMDEWMRDS SETNNLSEIY SSINIDGSNS VSVADPSFTS SAILDECFTL  660
KERK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	23	383	32	392	Auxin response factor 5
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj1g3v2155550.1

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_027356987.1	0.0	auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1S3E4Y9	0.0	A0A1S3E4Y9_CICAR; Auxin response factor
STRING	XP_004499235.1	0.0	(Cicer arietinum)

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]