PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc04g081240.2.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family ARF
Protein Properties Length: 931aa    MW: 103037 Da    PI: 5.3529
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc04g081240.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.51.5e-24147248199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++p++ ae+       ++++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD+v+F   
  Solyc04g081240.2.1 147 FCKTLTASDTSTHGGFSVPRRAAEKLfppldySMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGAKRLRAGDSVLFI-- 234
                         99*********************999*****9555554.49************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         ++++ +l+++v+r+
  Solyc04g081240.2.1 235 RDEKSQLLLGVRRA 248
                         45677789999997 PP

2Auxin_resp118.17.4e-39273356183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         aahaa+++s+F+++YnPra++seFv++++k++k+++ +++svGmRf m+fete+s +rr++Gt++g+sdldp+rWp SkWr+L+
  Solyc04g081240.2.1 273 AAHAAANRSTFTIFYNPRACPSEFVIPLAKYRKSIYnTQLSVGMRFGMMFETEESGKRRYMGTISGISDLDPLRWPSSKWRCLQ 356
                         79********************************99799********************************************7 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.4E-47134276IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-42140261IPR015300DNA-binding pseudobarrel domain
CDDcd100171.28E-22146247No hitNo description
PfamPF023625.4E-22147248IPR003340B3 DNA binding domain
SMARTSM010192.7E-24147249IPR003340B3 DNA binding domain
PROSITE profilePS5086313.211147249IPR003340B3 DNA binding domain
PfamPF065074.7E-34273356IPR010525Auxin response factor
PfamPF023093.9E-9810903IPR033389AUX/IAA domain
PROSITE profilePS5174525.992817901IPR000270PB1 domain
SuperFamilySSF542779.81E-9836896No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009908Biological Processflower development
GO:0009942Biological Processlongitudinal axis specification
GO:0010305Biological Processleaf vascular tissue pattern formation
GO:0048364Biological Processroot development
GO:0048507Biological Processmeristem development
GO:0005634Cellular Componentnucleus
GO:0016020Cellular Componentmembrane
GO:0042802Molecular Functionidentical protein binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 931 aa     Download sequence    Send to blast
MGSVEEKNKP GSLVSGAHTL LEEMKLLKEM QDHTGGGRKL ISSELWHACA GPLVTLPQVG  60
SLVYYFPQGH SEQVAVSTNR TATSQIPNYP NLASQLLCQV HNVTLHADKE TDEIYAQMSL  120
QPVNSEKDVF PIPDFGLKPN KHPTEFFCKT LTASDTSTHG GFSVPRRAAE KLFPPLDYSM  180
QPPTQELVVR DLHDNTWTFR HIYRGQPKRH LLTTGWSMFV GAKRLRAGDS VLFIRDEKSQ  240
LLLGVRRANR QQTSLPSSVL SADSMHIGVL AAAAHAAANR STFTIFYNPR ACPSEFVIPL  300
AKYRKSIYNT QLSVGMRFGM MFETEESGKR RYMGTISGIS DLDPLRWPSS KWRCLQVEWD  360
EPGCGDKQNR VSPWEVETPE SLFIFPSLTA GLKRPYQSTF LGAQTEWDSL MQHRPFMRVP  420
ENVYGDLQSS SISNLWSEQL MKMLIRPPPG LTGLQCGVPT VQDIKVALPQ EARNVVQPAG  480
NQKPELITVE ATPAQSETNS EVVLNQPVGV VNSISSQQAT LQAKSKPPEK VETDIIGKNS  540
EPRKETSNSS VKLDQFQCNE DKVAIKPASP HDLPTDASVT ASHHNSFSQL QASPWLIPHN  600
PQIDSAASNN ILQCPTNNEW NMSSLQSAAG LLKYPVSTST LTKHDNSFML PDTIGHGLAP  660
IGQDLWDHQL NDVKCFSQTN LQVPLDITNM QFLPDSYGFK DLSEESHNQS DIYSCLNFDS  720
NSGSTVIDNS VSSTVLDEFC NLKHTDFQNP SDFLLGNISS SQDVQSQITS ASLADSQNFS  780
VQEFADNSGG ASSSNVNFDE CNLLQNSSWQ QVAPRVRTYT KIQKTGSVGR SIDVSGFKNY  840
EELRSEIERM FGLEGLLNDT RGSSWKLVYV DFENDVLLVG DDPWEEFVGC VRCIRILSPT  900
EVQQMGEEGM QLLNSAGLQS INGSTSEFPN *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A0.013815392Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.75510.0flower| fruit| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In early embryo and during organ development.
UniprotTISSUE 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
UniProtAuxin 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
MP00153DAPTransfer from AT1G19850Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc04g081240.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM1952480.0Solanum lycopersicum auxin response factor 5 (ARF5) mRNA, complete cds
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001234545.10.0auxin response factor 5
SwissprotP930240.0ARFE_ARATH; Auxin response factor 5
TrEMBLA0A3Q7H3B00.0A0A3Q7H3B0_SOLLC; Auxin response factor
STRINGSolyc04g081240.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58592334
Representative plantOGRP82601216
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G19850.10.0ARF family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. Zhang Y, et al.
    Regulation of oncogene expression in T-DNA-transformed host plant cells.
    PLoS Pathog., 2015. 11(1): p. e1004620
    [PMID:25615824]
  7. Robert HS, et al.
    Plant embryogenesis requires AUX/LAX-mediated auxin influx.
    Development, 2015. 142(4): p. 702-11
    [PMID:25617434]
  8. 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]
  9. Ckurshumova W,Berleth T
    Overcoming recalcitrance - Auxin response factor functions in plant regeneration.
    Plant Signal Behav, 2015. 10(7): p. e993293
    [PMID:26098229]
  10. 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]
  11. Wu MF, et al.
    Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate.
    Elife, 2015. 4: p. e09269
    [PMID:26460543]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  25. Gaillochet C, et al.
    Control of plant cell fate transitions by transcriptional and hormonal signals.
    Elife, 2018.
    [PMID:29058667]
  26. 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]
  27. 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]