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 maker-scaffold06873-snap-gene-0.5-mRNA-1
Organism
Castanea mollissima
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Castanea
Family ARF
Protein Properties Length: 880aa    MW: 96935.9 Da    PI: 6.005
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
maker-scaffold06873-snap-gene-0.5-mRNA-1genomeTHGPView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B369.93.4e-22130231199
                                               EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE- CS
                                        B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvlt 62 
                                               f+k+lt sd++++g +++p++ ae++       + +++  ++l  +d++  sW++++iyr++++r++lt
  maker-scaffold06873-snap-gene-0.5-mRNA-1 130 FCKTLTASDTSTHGGFSVPRRAAEKIfppldysM-QPPA-QELGARDLHDSSWTFRHIYRGQPKRHLLT 196
                                               99*****************************954.5444.38*************************** PP

                                               TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                                        B3  63 kGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                                               +GW+ Fv+ ++L +gD+v+F   ++++ +l+++++r+
  maker-scaffold06873-snap-gene-0.5-mRNA-1 197 TGWSVFVSTKRLFAGDSVLFI--RDEKSQLLLGIRRA 231
                                               *********************..45677789999997 PP
2Auxin_resp123.51.4e-40256338183
                                Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdl 69 
                                               aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s  rr++Gt++g+sdl
  maker-scaffold06873-snap-gene-0.5-mRNA-1 256 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITGISDL 324
                                               79******************************************************************* PP

                                Auxin_resp  70 dpvrWpnSkWrsLk 83 
                                               d+vrW+nS+Wr+L+
  maker-scaffold06873-snap-gene-0.5-mRNA-1 325 DTVRWKNSQWRNLQ 338
                                               ************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.45E-44120259IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.6E-41122245IPR015300DNA-binding pseudobarrel domain
CDDcd100171.06E-18129230No hitNo description
SMARTSM010194.2E-22130232IPR003340B3 DNA binding domain
PfamPF023624.5E-20130231IPR003340B3 DNA binding domain
PROSITE profilePS5086311.914130232IPR003340B3 DNA binding domain
PfamPF065078.9E-36256338IPR010525Auxin response factor
PfamPF023092.0E-9751840IPR033389AUX/IAA domain
PROSITE profilePS5174524.674754847IPR000270PB1 domain
SuperFamilySSF542771.47E-8767832No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0010311Biological Processlateral root formation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 880 aa     Download sequence    Send to blast
MTFDVSYDGN NIFFGLSTGE KKSINSELWH ACAGPLVSLP PVGSLVVYFP QGHSEQVAAS  60
MQKETDFIPN YPNLPSKLIC MLHNVTLHAD PETDEVYAQM TLLPVNKYDK EALLASDMGL  120
KQSKQPAEFF CKTLTASDTS THGGFSVPRR AAEKIFPPLD YSMQPPAQEL GARDLHDSSW  180
TFRHIYRGQP KRHLLTTGWS VFVSTKRLFA GDSVLFIRDE KSQLLLGIRR ANRQQPALSS  240
SVISSDSMHI GILAAAAHAA ANNSPFTIFY NPRASPSEFV IPLAKYNKAM YTQVSLGMRF  300
RMMFETEESG VRRYMGTITG ISDLDTVRWK NSQWRNLQVF FGLVHWVGWD ESTAGERPSR  360
VSIWEIEPVV TPFYICPPPF FRPKFPRQPG MPDDESDIEN AFKRAMPWLG DEFGMKDAPS  420
SIFPGLSLVQ WMSMQQNNQF SAAQSGLFPS MVSSNGLHNN LNADDPSKLL SFQAPAIFNN  480
SKYSQAIPNH SRVSTLIAPA AGTVTTVPTT IVATKPVTAS TAADTNATPQ SQHKPLTAIR  540
AHSGLTEGDA PSCSTSPSTN NCQVSPSNLL NRNQQGSAML VGDSLIEPPS NLLQELQSKS  600
DIRIKHELPS SKGPDQIKYK STITDQLEAS SSGTSYCLDA SIPQNFPIPT FGLEGDVQSH  660
PRNNLPFATN IDGLAPDTLL SRGYDSQKDL QNLLSNYGGT PRDIETELST AAISSQSFGV  720
PNIPFKPGCS SDVAINDAGV LSNGLWANQT QRMRTYTKVQ KRGSVGRCID VTRYKEYDEL  780
RHDLARMFGI EGQLEDPQRT DWKLVYVDHE NDILLVGDDP WEEFVSCVQS IKILSSAEVQ  840
QMSLDGDLGH VPVSNQACSG TDSGNAWRPY EDNSAASFNR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1691736744388Auxin 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_012851206.10.0PREDICTED: auxin response factor 19-like
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A103Y2650.0A0A103Y265_CYNCS; Auxin response factor
STRINGLus100336350.0(Linum usitatissimum)
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]