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.008G210200.4
Common NameB456_008G210200, LOC105764826
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: 850aa    MW: 94578.4 Da    PI: 7.0405
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.008G210200.4genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.41.3e-23154255199
                         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.008G210200.4 154 FCKILTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL-- 241
                         99*****************************7333.34459************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Gorai.008G210200.4 242 RGENGELRVGVRRA 255
                         449999*****996 PP
2Auxin_resp118.17.2e-39280362183
          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.008G210200.4 280 AWHAFTTKTIFTVYYKPRTSPAEFIVPFGQYMESLKNNYSIGMRFKMRFEGEEAPEQRFTGTVVGIEDADPKRWQDSKWRCLK 362
                         79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.57E-40148283IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.7E-41150269IPR015300DNA-binding pseudobarrel domain
CDDcd100178.49E-22152254No hitNo description
PfamPF023621.3E-21154255IPR003340B3 DNA binding domain
PROSITE profilePS5086312.125154256IPR003340B3 DNA binding domain
SMARTSM010192.7E-23154256IPR003340B3 DNA binding domain
PfamPF065071.7E-35280362IPR010525Auxin response factor
PfamPF023092.2E-10709811IPR033389AUX/IAA domain
SuperFamilySSF542773.68E-12720806No hitNo description
PROSITE profilePS5174521.527726810IPR000270PB1 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: 850 aa     Download sequence    Send to blast
MKGNCVNVRG GESCSSGYSE SMDARKTMEG QNGHSTHQAA IRDPETALYT ELWHACAGPL  60
VTVPREGERV FYFPQGHIEQ VEASTNQVPD QHMPVYNLPS KILCRVINVQ LKAEPDTDEV  120
FAQVTLLPEP TQDENTVDKE SPVPQPPRFH VHSFCKILTA SDTSTHGGFS VLRRHADECL  180
PPLDMSRQPP TQELVAKDLH GNEWRFRHIF RGQPRRHLLQ SGWSVFVSSK RLVAGDAFIF  240
LRGENGELRV GVRRAMRQQG NVPSSVISSH SMHLGVLATA WHAFTTKTIF TVYYKPRTSP  300
AEFIVPFGQY MESLKNNYSI GMRFKMRFEG EEAPEQRFTG TVVGIEDADP KRWQDSKWRC  360
LKVRWDETSS IPRPERVSPW KIEPPLAPPA LNPLPMPRTK RPRSHAVPSS PDSSVLTREG  420
SSKVTIDPSS ASGLSRVLQG QEFSTLRGNF AESIESDTAE KSVMWPPSVD DKNNDVVSAS  480
RRFPSENWMS SGRHERTCTD LLTGFGSNAE SLHGYCSSLV DQTLVAGNST RKQSLHQEGK  540
LGSWSLMPSG LSLKLADTNA KSPLQGSDVP YQMRGNGRCS GFDDYPILQG HRIEHSHGNW  600
LMPPPTSSHH ESNPVQSRDL MPKTSFVQGH ENGKYREGNC KLFGIPLIRN SVASEPTVSH  660
TNALSKPVAH MQAASHQVLE FVSAQNSEKL KVLQLAEVED LSNYNEQEKQ PRTREIQSKP  720
SSASTRSCTK VHKQGIALCR SVDLTKFNDY DELIAELDGL FEFKGELMAP KKNWLVVYTD  780
DEGDMMLVGD DPWQEFCAMV RKIGIYTREE VQKMKPGSLS SKGEDNSVST GGVDGKEMMC  840
PSASSAENC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1804738418354Auxin response factor 1
4ldw_A1e-1804738418354Auxin response factor 1
4ldw_B1e-1804738418354Auxin 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
TrEMBLA0A0D2PYS70.0A0A0D2PYS7_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]