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 Tp57577_TGAC_v2_mRNA13127
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family ARF
Protein Properties Length: 1139aa    MW: 128233 Da    PI: 7.0398
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA13127genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B368.21.2e-21126227199
                                EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT- CS
                         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegD 78 
                                f+k+lt sd++++g +++p++ ae++      +++++  ++l+ +d++ ++W +++iyr++++r++lt+GW+ F + ++L +gD
  Tp57577_TGAC_v2_mRNA13127 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVAKDLHDNTWAFRHIYRGQPKRHLLTTGWSVFISTKRLFAGD 208
                                99*****************************9445444.38******************************************* PP

                                EEEEEE-SSSEE..EEEEE-S CS
                         B3  79 fvvFkldgrsefelvvkvfrk 99 
                                +v+F   ++++++l+++++r+
  Tp57577_TGAC_v2_mRNA13127 209 SVLFI--RDEKQQLLLGLRRA 227
                                *****..56788899999986 PP
2Auxin_resp124.66.7e-41252334183
                 Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                                aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s  rr++Gtv+g+sdldpvrW+nS+Wr+L+
  Tp57577_TGAC_v2_mRNA13127 252 AAHAAANNSPFTIYYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTVTGISDLDPVRWKNSQWRNLQ 334
                                79*******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.23E-44116255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.3E-40118241IPR015300DNA-binding pseudobarrel domain
CDDcd100172.75E-17125217No hitNo description
PROSITE profilePS5086311.885126228IPR003340B3 DNA binding domain
SMARTSM010192.7E-21126228IPR003340B3 DNA binding domain
PfamPF023628.0E-20126227IPR003340B3 DNA binding domain
PfamPF065077.3E-36252334IPR010525Auxin response factor
PfamPF023093.1E-910041096IPR033389AUX/IAA domain
PROSITE profilePS5174525.02810101103IPR000270PB1 domain
SuperFamilySSF542771.57E-810231088No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009725Biological Processresponse to hormone
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 1139 aa     Download sequence    Send to blast
MKAPSNGYLP NSGDGERKTI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPSYPNL PSKLICMLHN VALHADPETD EVYAQMTLQP VNKYDKEAIL ASDFGLKQNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELVAKD LHDNTWAFRH  180
IYRGQPKRHL LTTGWSVFIS TKRLFAGDSV LFIRDEKQQL LLGLRRANRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS PFTIYYNPRA SPSEFVIPLA KYNKAMYTQV SLGMRFRMMF  300
ETEESGVRRY MGTVTGISDL DPVRWKNSQW RNLQIGWDES TAGERPSRVS IWDIEPVVTP  360
FYICPPPFFR PKFPRQPGMP DDDSDVENAF KRAMPWLGDD FGMKDASSSG FPGLSLVQWM  420
QMQQNNQFSA AQSGCFPSML SSNTLHGNLS TDDPSKLLSF QAPGLSAPSL QFNKPNLPNQ  480
TNQLHQSPTS WPQQQQQQQL QNLQQQQQQQ LQNLQQQQQQ QLQQQQQQQL QSLSQIPMNQ  540
FQQQRQQQLP ESQNLTLLQQ QMSQQLGQQP QKQPQSSQQA ILNNGIVASN QNTNQFAQQQ  600
TLAYTQLQQK QQLLPGSIPL QQSTQSASKN TFPLTSLPQD SQFHQHIDQQ PSLLQRQQQQ  660
TQLQQSSLQA LQQSQPQWVP PNLSVTQMSQ QNTSEQQLQL QFLHKLQQQQ QQQQQXXXXX  720
XXXXXXXXXX XXXXXXXXXN NFFQHLAHFC NLSFYRNKIL TNKTSNYRRC LYPNIIINSL  780
AITHFQRRSK PRTITRVPST LTDGEAPSCS TSPSTNNCQI SQPNLLKRNQ QVQTTIGGXX  840
XXXXXXXXXX XXXKSDMHIK QEFSNVKGPD QLKYKGATTD QLEASSGTSY CLDPGNVQQS  900
LPLSNFCMES DVQSNPRNTL PFETNFDGLM SDTMLSRGYD SQKDLQNLLA NYCGAPGDIE  960
TELSTADISS QSFGLPDLAF KPGCSNDVGI DDTSGVLNNG VRANQTQRMR TYTKVQKRGS  1020
VGRCIDVTRY KGYDELRYDL ARMFGIEGQL EDPQRTDWKL VYVDHENDIL LVGDDPWEEF  1080
VSCVQSIKIL SSAEVQQMSL DGDLGGNVPI PNQASSGTDS GNAWRGQYDD NSAASFNR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1711535545388Auxin 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp57577_TGAC_v2_mRNA13127
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_004508019.10.0auxin response factor 19 isoform X2
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A1S2YPR00.0A0A1S2YPR0_CICAR; Auxin response factor
STRINGXP_004508018.10.0(Cicer arietinum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF49183352
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. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]