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 Gh_D12G1909
Organism
Gossypium hirsutum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family ARF
Protein Properties Length: 841aa    MW: 93719.2 Da    PI: 6.8131
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gh_D12G1909genomeNAU-NBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.51.3e-23155256199
                  EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                  f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el
  Gh_D12G1909 155 FCKILTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGEL 249
                  99*****************************7333.34459************************************************..449999* PP

                  EEEEE-S CS
           B3  93 vvkvfrk 99 
                  +v+v+r+
  Gh_D12G1909 250 RVGVRRA 256
                  ****996 PP
2Auxin_resp118.17.1e-39281363183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  a+ha++tk++F+v+Y+Pr+s++eF+v++ +++++lk+++s+GmRfkm+fe+e+++e+r++Gtvvg++d+dp rW++SkWr+Lk
  Gh_D12G1909 281 AWHAFTTKTIFTVYYKPRTSPAEFIVPFGQYMESLKNNYSIGMRFKMRFEGEEAPEQRFTGTVVGIEDADPKRWQDSKWRCLK 363
                  79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.1E-40150284IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.6E-41151270IPR015300DNA-binding pseudobarrel domain
CDDcd100178.34E-22153255No hitNo description
PROSITE profilePS5086312.125155257IPR003340B3 DNA binding domain
PfamPF023621.3E-21155256IPR003340B3 DNA binding domain
SMARTSM010192.7E-23155257IPR003340B3 DNA binding domain
PfamPF065071.7E-35281363IPR010525Auxin response factor
PfamPF023092.5E-9698803IPR033389AUX/IAA domain
PROSITE profilePS5174518.943718802IPR000270PB1 domain
SuperFamilySSF542771.57E-10719798No 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: 841 aa     Download sequence    Send to blast
MKGNCVNVRG GESCSSGYSK SMDARKTMEG QNGHSTHQAA IRDPETALYT ELWHACAGPL  60
VTVPREGESV FYFPQGHIEQ VEASTNQVPD QHMPVYNLPS KILCRVINVQ LKAEPDTDEV  120
FAQVTLLPEP TQQDENTVDK ESPFPQPPRF HVHSFCKILT ASDTSTHGGF SVLRRHADEC  180
LPPLDMSRQP PTQELVAKDL HGNEWRFRHI FRGQPRRHLL QSGWSVFVSS KRLVAGDAFI  240
FLRGENGELR VGVRRAMRQE GNVPSSVISS HSMHLGVLAT AWHAFTTKTI FTVYYKPRTS  300
PAEFIVPFGQ YMESLKNNYS IGMRFKMRFE GEEAPEQRFT GTVVGIEDAD PKRWQDSKWR  360
CLKVRWDETS SIPRPERVSP WKIEPPLAPP ALNPLPMPRT KRPRSHAVPS SPDSSVLTRE  420
GSSKVTIDPS SASGLSRVLQ GQEFSTLRSN FAESIESDIA EKSVMWPPSV DDNNNDVVSA  480
SRRFASENWM SSGRHERPCT DLLTGFGSNA ESLHGYCSSL VDQTLVAGNS TRKQSLHQEG  540
KLGSWSLMPS GQSLKLADTN AKSPLQGSDV PYQMRGNGRC SGFDDYPILQ GHRIEHSHGN  600
WLMPPPTSSH HESNPVQSRD LMPKTSFVQG HENGKYREGN CKLFGIPLIR NSVASEPTVS  660
HMQAASRQVL EFESAQNSEK LKALQLAEVE DLSNYNEQEK QPHTREIQSK PSSASTRSCT  720
KVVHKQGIAL GRSVDLTKFN DYDELIAELD GLFEFKGELM APKKNWLVVY TDDEGDMMLV  780
GDDPWLEFCA MVRKIGIYTR EEVQKMKPGS LSSKGEDNSV STGGVDGKEM MCPSASSAEN  840
C
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1784738518354Auxin response factor 1
4ldw_A1e-1784738518354Auxin response factor 1
4ldw_B1e-1784738518354Auxin response factor 1
4ldx_A1e-1774738518354Auxin response factor 1
4ldx_B1e-1774738518354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ghi.66890.0boll| leaf| ovule| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression increases at the orange (Or) and red (R) fruit stages. Expression is increased with ethylene at mature green (MG) stage, but only after six days post-treatment. Expression is increased three days post-treatment with plant hormone abscisic acid (ABA) at the Or stage, but not at the MG or breaker (Br) stages. No change in expression level up to six days post-treatment with ABA at the MG fruit stage (PubMed:26959229). Expressed during floral development (PubMed:21735233, PubMed:28167023, PubMed:27645097). During bud-anthesis stages flowers exhibit dynamic expression pattern in sepal, stamen, ovary and petal (PubMed:28167023). Expressed during ovary development with the highest expression on the third day after the flower fully opened (PubMed:21735233). During seed germination, expressed in the cotyledon. Expressed strongly in the pollen grain. Expressed in the developing fruits, in which mainly expressed in the vascular tissues and seeds. During growth, strongly expressed in leaf, where mainly expressed in the trichome and in the root tip and lateral root formation sites. Expressed in the vascular tissue and the epicycle of the root. Also expressed in branch (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
UniprotTISSUE SPECIFICITY: Expressed in root, leaf and flower (PubMed:26716451, PubMed:27645097, PubMed:28167023, PubMed:21735233). Expressed in flower buds about three days before opening including ovary, petal and sepal with the highest in stamen (PubMed:21735233). Expressed in stem (PubMed:26716451, PubMed:28167023, PubMed:21735233). Expressed in fruit (PubMed:26716451, PubMed:27645097, PubMed:28167023). Expressed in seeds (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
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}.
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016736497.10.0PREDICTED: auxin response factor 2-like isoform X1
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A1U8NBV10.0A0A1U8NBV1_GOSHI; Auxin response factor
STRINGGorai.008G210200.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
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]