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 evm_27.model.AmTr_v1.0_scaffold00007.382
Common NameAMTR_s00007p00267580
Organism
Amborella trichopoda
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family ARF
Protein Properties Length: 931aa    MW: 104541 Da    PI: 7.0449
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00007.382genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.99e-24107208199
                                               EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-T CS
                                        B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltk 63 
                                               f+k+lt sd++++g +++p++ ae++      +++++  ++l+ +d++ ++W++++iyr++++r++lt+
  evm_27.model.AmTr_v1.0_scaffold00007.382 107 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVARDLHDNVWKFRHIYRGQPKRHLLTT 174
                                               99*****************************9445444.38**************************** PP

                                               THHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                                        B3  64 GWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                                               GW+ Fv+a++L +gD+v+F   ++++ +l+++v+r+
  evm_27.model.AmTr_v1.0_scaffold00007.382 175 GWSVFVSAKRLFAGDSVIFI--RDEKSQLCLGVRRA 208
                                               ********************..45677789999997 PP
2Auxin_resp120.61.2e-39233316183
                                Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsd 68 
                                               aahaa+++s+F+++YnPras+seFv++++k++ka++ ++vs+GmRf+m+feteds  rr++Gt++g+sd
  evm_27.model.AmTr_v1.0_scaffold00007.382 233 AAHAAANNSPFSIFYNPRASPSEFVIPLSKYNKAIYgTQVSPGMRFRMMFETEDSGVRRYMGTITGISD 301
                                               79**********************************9******************************** PP

                                Auxin_resp  69 ldpvrWpnSkWrsLk 83 
                                               ldp+rW++S+Wr+L+
  evm_27.model.AmTr_v1.0_scaffold00007.382 302 LDPIRWKGSPWRNLQ 316
                                               *************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.57E-4497236IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.4E-4299222IPR015300DNA-binding pseudobarrel domain
CDDcd100172.65E-21106207No hitNo description
PROSITE profilePS5086312.351107209IPR003340B3 DNA binding domain
PfamPF023621.1E-21107208IPR003340B3 DNA binding domain
SMARTSM010198.5E-25107209IPR003340B3 DNA binding domain
PfamPF065075.1E-34233316IPR010525Auxin response factor
PROSITE profilePS5174516.579842927IPR000270PB1 domain
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: 931 aa     Download sequence    Send to blast
MLVPAHSCLY LQLAVLWYIS HKDTVNRYII TTVTASMQKG MDGQIPNYPN LPSKLVCLLH  60
NVTLHADTET DEVYAQMTLQ PVNKNDKDML LASDFGLKQS KQPTEFFCKT LTASDTSTHG  120
GFSVPRRAAE KIFPPLDFSM QPPAQELVAR DLHDNVWKFR HIYRGQPKRH LLTTGWSVFV  180
SAKRLFAGDS VIFIRDEKSQ LCLGVRRANR QLPTLSSSVL SSDSMHIGIL AAAAHAAANN  240
SPFSIFYNPR ASPSEFVIPL SKYNKAIYGT QVSPGMRFRM MFETEDSGVR RYMGTITGIS  300
DLDPIRWKGS PWRNLQVGWD ESIAGERQNR VSVWEIEPVA TPFYICPPPF FRPQNPGQPG  360
MQDDIETENV FKRAMPWLND DISVKDFQNI LPGYSLFQWM SMRQNPQLGA QASQADYLST  420
TPPRVRNLNI DDPSKQLNFQ THFQPPHTLQ FNLPKVPQLT QQHTGHLQQQ QQPAPMNLQT  480
QVHPQVVTNQ PHKEQSSVVN QPLGHNQIHN QILQQNFIQN QQSHLQSHQN ISQSALYQHQ  540
LLQPQVEQQH NNNLQQQQVQ QLHMLQKLQQ QQQEQLIPQF RSSLSQNQSP QSQLSENQQH  600
QASQQQLNSN QFSQSLHNHD QNKRQQLIQS ADISAQLQPL LSQIQARAHS GHTDGDPSSC  660
STSPSTNNCS ASSGFLIKTQ ELTQAVTNTV QDQQLNGQIK NGPRGSNHLE ELSSTANYGL  720
DGGFHQSSPM PSFHQSAYLG SQDSDLAFDP RNNLLFGVSI DGTLAPDSLL SRGIASGKDL  780
QSMISGYESP KDMETDISTA ISSQSFGVPD ISFTPGCSSD ARLSDGAMAN RGPWPPHQLC  840
MRTYTKVQKR GSVGRLIDVT RYKGYDELRR GLACMFGMEG QLEDPHQSGW KLVYVDKENE  900
TLLVGDDPWV LYEARTQLVL DLTLFPPPTY *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1533333784388Auxin response factor 5
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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16461383, ECO:0000269|PubMed:17259263}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and ethylene. {ECO:0000269|PubMed:16461383}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011623129.10.0auxin response factor 19 isoform X1
RefseqXP_020522402.10.0auxin response factor 19 isoform X1
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLW1PD690.0W1PD69_AMBTC; Auxin response factor
STRINGERN055710.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP41931125
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G19220.10.0auxin response factor 19
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Perilli S, et al.
    RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling.
    Plant Cell, 2013. 25(11): p. 4469-78
    [PMID:24285791]
  3. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  4. Sun Y, et al.
    Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas.
    Sci Rep, 2017. 7: p. 40844
    [PMID:28102350]
  5. 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]
  6. Olmo R, et al.
    Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?
    Front Plant Sci, 2017. 8: p. 875
    [PMID:28603536]
  7. Lee K,Seo PJ
    High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis.
    Planta, 2017. 246(4): p. 797-802
    [PMID:28766014]
  8. Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J
    Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana.
    Plant Sci., 2017. 264: p. 168-178
    [PMID:28969797]
  9. Nakamura M, et al.
    Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells.
    Plant Physiol., 2018. 176(1): p. 378-391
    [PMID:29084900]
  10. Hong L, et al.
    Alternative polyadenylation is involved in auxin-based plant growth and development.
    Plant J., 2018. 93(2): p. 246-258
    [PMID:29155478]
  11. Lee K,Park OS,Seo PJ
    Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.
    Sci Signal, 2018.
    [PMID:29184030]
  12. Kimura T, et al.
    Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis.
    Plant Cell Physiol., 2018. 59(4): p. 823-835
    [PMID:29401292]
  13. Schoenaers S, et al.
    The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth.
    Curr. Biol., 2018. 28(5): p. 722-732.e6
    [PMID:29478854]
  14. Huang KL, et al.
    The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots.
    Plant Physiol., 2018. 178(1): p. 413-427
    [PMID:30026290]