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 Gorai.008G210200.9
Common NameB456_008G210200
Organism
Gossypium raimondii
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: 759aa    MW: 84605.4 Da    PI: 7.4869
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.008G210200.9genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.71.1e-2363164199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   
  Gorai.008G210200.9  63 FCKILTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL-- 150
                         99*****************************7333.34459************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Gorai.008G210200.9 151 RGENGELRVGVRRA 164
                         449999*****996 PP
2Auxin_resp118.36.2e-39189271183
          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
  Gorai.008G210200.9 189 AWHAFTTKTIFTVYYKPRTSPAEFIVPFGQYMESLKNNYSIGMRFKMRFEGEEAPEQRFTGTVVGIEDADPKRWQDSKWRCLK 271
                         79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.31E-4057192IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.2E-4159178IPR015300DNA-binding pseudobarrel domain
CDDcd100178.96E-2261163No hitNo description
PROSITE profilePS5086312.12563165IPR003340B3 DNA binding domain
SMARTSM010192.7E-2363165IPR003340B3 DNA binding domain
PfamPF023621.1E-2163164IPR003340B3 DNA binding domain
PfamPF065071.5E-35189271IPR010525Auxin response factor
SuperFamilySSF542773.14E-12629715No hitNo description
PROSITE profilePS5174521.527635719IPR000270PB1 domain
PfamPF023096.5E-7681720IPR033389AUX/IAA 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: 759 aa     Download sequence    Send to blast
MPVYNLPSKI LCRVINVQLK AEPDTDEVFA QVTLLPEPTQ QDENTVDKES PVPQPPRFHV  60
HSFCKILTAS DTSTHGGFSV LRRHADECLP PLDMSRQPPT QELVAKDLHG NEWRFRHIFR  120
GQPRRHLLQS GWSVFVSSKR LVAGDAFIFL RGENGELRVG VRRAMRQQGN VPSSVISSHS  180
MHLGVLATAW HAFTTKTIFT VYYKPRTSPA EFIVPFGQYM ESLKNNYSIG MRFKMRFEGE  240
EAPEQRFTGT VVGIEDADPK RWQDSKWRCL KVRWDETSSI PRPERVSPWK IEPPLAPPAL  300
NPLPMPRTKR PRSHAVPSSP DSSVLTREGS SKVTIDPSSA SGLSRVLQGQ EFSTLRGNFA  360
ESIESDTAEK SVMWPPSVDD KNNDVVSASR RFPSENWMSS GRHERTCTDL LTGFGSNAES  420
LHGYCSSLVD QTLVAGNSTR KQSLHQEGKL GSWSLMPSGL SLKLADTNAK SPLQGSDVPY  480
QMRGNGRCSG FDDYPILQGH RIEHSHGNWL MPPPTSSHHE SNPVQSRDLM PKTSFVQGHE  540
NGKYREGNCK LFGIPLIRNS VASEPTVSHT NALSKPVAHM QAASHQVLEF VSAQNSEKLK  600
VLQLAEVEDL SNYNEQEKQP RTREIQSKPS SASTRSCTKV HKQGIALCRS VDLTKFNDYD  660
ELIAELDGLF EFKGELMAPK KNWLVVYTDD EGDMMLVGDD PWQEFCAMVR KIGIYTREEV  720
QKMKPGSLSS KGEDNSVSTG GVDGKEMMCP SASSAENC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-153129364354Auxin response factor 1
4ldw_A1e-153129364354Auxin response factor 1
4ldw_B1e-153129364354Auxin response factor 1
4ldx_A1e-153129364354Auxin response factor 1
4ldx_B1e-153129364354Auxin response factor 1
Search in ModeBase
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}.
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_012439048.10.0PREDICTED: auxin response factor 2-like isoform X1
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A0D2RJD30.0A0A0D2RJD3_GOSRA; Auxin response factor
TrEMBLA0A0D2T4660.0A0A0D2T466_GOSRA; Auxin response factor
STRINGGorai.008G210200.10.0(Gossypium raimondii)
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. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  3. 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]
  4. Xu T, et al.
    SlARF2a plays a negative role in mediating axillary shoot formation.
    Sci Rep, 2016. 6: p. 33728
    [PMID:27645097]
  5. 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]