PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Phvul.009G161900.1
Common NamePHAVU_009G161900g
Organism
Phaseolus vulgaris
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
Family ARF
Protein Properties Length: 844aa    MW: 93731.4 Da    PI: 6.3976
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Phvul.009G161900.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.81e-23142243199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++ +++a+e+      + k++ +++l  +d++g++W++k+i+r++++r++l++GW+ Fv++++L +gD ++F   
  Phvul.009G161900.1 142 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-KQPPTQELAAKDLHGNEWRFKHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL-- 229
                         99*****************************63.4445569************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Phvul.009G161900.1 230 RGENGELRVGVRRA 243
                         449999*****996 PP
2Auxin_resp118.74.8e-39268350183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         a+ha+ t+++F+v+Y+Pr+s++eF+v++++++++lk+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW++SkWr+Lk
  Phvul.009G161900.1 268 AWHAILTGTIFTVYYKPRTSPAEFIVPYDQYMESLKNSYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPNRWRESKWRCLK 350
                         79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019369.16E-40138271IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.105.0E-41139257IPR015300DNA-binding pseudobarrel domain
CDDcd100175.61E-21140242No hitNo description
PROSITE profilePS5086311.843142244IPR003340B3 DNA binding domain
SMARTSM010198.9E-23142244IPR003340B3 DNA binding domain
PfamPF023621.2E-21142243IPR003340B3 DNA binding domain
PfamPF065077.4E-36268350IPR010525Auxin response factor
PfamPF023092.8E-12704803IPR033389AUX/IAA domain
PROSITE profilePS5174524.364715797IPR000270PB1 domain
SuperFamilySSF542771.86E-11715792No 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 844 aa     Download sequence    Send to blast
MASSEVTMKG NCLNHIDGGA SEAQSPATAK DAEAALFREL WHACAGPLVT VPREGERVFY  60
FPQGHIEQVE ASTNQVADQH MPVYDLPPKI LCRVINVQLK AEPDTDEVFA QVTLLPEPNQ  120
NENDVEKEPP PPPPPRFHVH SFCKTLTASD TSTHGGFSVL RRHADECLPP LDMSKQPPTQ  180
ELAAKDLHGN EWRFKHIFRG QPRRHLLQSG WSVFVSSKRL VAGDAFIFLR GENGELRVGV  240
RRAMRQQGNV PSSVISSHSM HLGVLATAWH AILTGTIFTV YYKPRTSPAE FIVPYDQYME  300
SLKNSYSIGM RFKMRFEGEE APEQRFTGTI VGIEDSDPNR WRESKWRCLK VRWDETSNTP  360
RPERVSPWKI EPALAPPALN PLSMPRPKRP RSNAIPPSPD SSVLTREASS KVSIDPSPAN  420
GFPRVLQGQE FSTLRGNYTE SIDSDAAEKS VVWPPAAVDD EKIDVSTSRR YGSESWMSMG  480
RNEPTYSDLL SGFGAGGDSS HSSFMDQMSP VAYPTRKQSS DHEGKLHMPQ PWPVMPSSLS  540
LNILDSNTKG PAHGGDPTYQ ARGNLRYSAF GEYPALHGHK VEHSHGNLMP PPPPAPVNQY  600
QIPCSRELML KPVPAKTFEA VKLKDGDCKL FGFSLISGPI VPEPPVSQRN MNEPTGQMHL  660
TPHQQRTSEN DEKSDHSKGS KTADDLIVDD HDRPLQASQL HAKDGQAKPL SSSARSCTKV  720
HKKGIALGRS VDLTKYTGYD ELVAELDQLF EFEGELLSTK KDWLIVYTDN EGDMMLVGDD  780
PWQEFCAMVR KIYIYPKEEI QKMSPGTLSS KNEENQSGSE GADAKDVKCL PPQKFNYENG  840
LDA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1783537218354Auxin response factor 1
4ldw_A1e-1783537218354Auxin response factor 1
4ldw_B1e-1783537218354Auxin response factor 1
4ldx_A1e-1783537218354Auxin response factor 1
4ldx_B1e-1783537218354Auxin response factor 1
Search in ModeBase
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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255|RuleBase:RU004561, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPhvul.009G161900.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150350.0AP015035.1 Vigna angularis var. angularis DNA, chromosome 2, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007137862.10.0hypothetical protein PHAVU_009G161900g
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLV7B0420.0V7B042_PHAVU; Auxin response factor
STRINGXP_007137862.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF32813366
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  2. Breitel DA, et al.
    AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening.
    PLoS Genet., 2016. 12(3): p. e1005903
    [PMID:26959229]
  3. Xu T, et al.
    SlARF2a plays a negative role in mediating axillary shoot formation.
    Sci Rep, 2016. 6: p. 33728
    [PMID:27645097]
  4. Ren Z,Liu R,Gu W,Dong X
    The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence.
    Plant Sci., 2017. 256: p. 103-111
    [PMID:28167023]