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 AHYPO_003480-RA
Organism
Amaranthus hypochondriacus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Amaranthaceae; Amaranthus
Family ARF
Protein Properties Length: 838aa    MW: 93199.4 Da    PI: 6.7065
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AHYPO_003480-RAgenomeBYUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.65.8e-24138239199
                      EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                      f+k+lt sd++++g +++ +++a+e+      +  ++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +
  AHYPO_003480-RA 138 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-RQPPTQELMAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGE 228
                      99*****************************73.3334459************************************************..449 PP

                      EE..EEEEE-S CS
               B3  89 efelvvkvfrk 99 
                      ++el+v+v+r+
  AHYPO_003480-RA 229 NGELRVGVRRA 239
                      999*****996 PP
2Auxin_resp120.51.3e-39264346183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                      a+ha +++++F+v+Y+Pr+s+++F+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vgv+d+dp rW++SkWr+Lk
  AHYPO_003480-RA 264 AWHAYNSGTMFTVYYKPRTSPAQFIVPYDQYMESVKNQYSIGMRFKMRFEGEEAPEQRFTGTIVGVEDADPNRWRDSKWRCLK 346
                      79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.6E-41131253IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.61E-41134267IPR015300DNA-binding pseudobarrel domain
CDDcd100175.98E-21136238No hitNo description
PROSITE profilePS5086311.914138240IPR003340B3 DNA binding domain
SMARTSM010192.3E-23138240IPR003340B3 DNA binding domain
PfamPF023621.0E-21138239IPR003340B3 DNA binding domain
PfamPF065072.1E-36264346IPR010525Auxin response factor
PfamPF023091.4E-13664802IPR033389AUX/IAA domain
PROSITE profilePS5174523.509711795IPR000270PB1 domain
SuperFamilySSF542771.81E-12712788No hitNo description
Gene3DG3DSA:3.10.20.2406.7E-4732787No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 838 aa     Download sequence    Send to blast
MSLSEVSIKA TADKAGEQVS VAGKGAVVDP ETALYKELWH ACAGPLVTVP RINELVYYFP  60
QGHIEQVEAS TNQGAEQQMP VYNLPWKILC RVIDVQLKAE PDTDEVYAQI MLLPQGNENS  120
GEKESSPVLQ PHFHVHSFCK TLTASDTSTH GGFSVLRRHA DECLPPLDMS RQPPTQELMA  180
KDLHGNEWRF RHIFRGQPRR HLLQSGWSVF VSSKRLVAGD AFIFLRGENG ELRVGVRRAM  240
RQQGVVPSSV ISSHSMHLGV LATAWHAYNS GTMFTVYYKP RTSPAQFIVP YDQYMESVKN  300
QYSIGMRFKM RFEGEEAPEQ RFTGTIVGVE DADPNRWRDS KWRCLKVRWD ETSAIPRPDR  360
VSPWQIEPAL SPPTVNPLPM TRGKRPRANV MTQSSDSSVL TREGFSKVVA DPSPVGGFSR  420
VLQGQEYSAL KPSLADSNES DTVEKPNAWS NSVDEGKVDN ANGSLKYRSE NFMPSMRSEP  480
AFADLLSGFG VQNETASGSH APYQTTASSP MKKHMLDQDV KFNMLGGSWS IMPANLSLNL  540
SESSMKLHSP SGNVSYQGQG SARYVGGFSE MQMIRNHRID HQNGSWLMPP PPSYFDNHTQ  600
SRDAVTHPSQ IEQEPNKPKD GSYKLFGIPL ISSPTTQDSS ILSRSVFEPA THISPVSHRL  660
HNSDSDQSSE QSKSSKQMDC VPPCSEQEKK MPNSQSLSRD AQAKAHGGSS RSCTKVHKQG  720
IALGRSVDLS KFSNYDQLVE ELDCLFDFNG ELKTPEKNWL IVYTDDEGDM MLVGDDPWQE  780
FVGMVRKIFI YTKEEVQKMA PRTLNFRNED NVPTTGGSDS KEAKQSIPSS ASNAESH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1763336818354Auxin response factor 1
4ldw_A1e-1763336818354Auxin response factor 1
4ldw_B1e-1763336818354Auxin response factor 1
4ldx_A1e-1763336818354Auxin response factor 1
4ldx_B1e-1763336818354Auxin 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010678349.10.0PREDICTED: auxin response factor 2
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLD7SH690.0D7SH69_VITVI; Auxin response factor
STRINGXP_010678349.10.0(Beta vulgaris)
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]