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.001G054600.1
Common NameB456_001G054600, LOC105785774
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: 861aa    MW: 95416.9 Da    PI: 6.5549
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.001G054600.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.89.8e-24162263199
                         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.001G054600.1 162 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL-- 249
                         99*****************************7333.34459************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Gorai.001G054600.1 250 RGENGELRVGVRRA 263
                         449999*****996 PP
2Auxin_resp119.92e-39288370183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         a+ha +tk++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp +W++SkWr+Lk
  Gorai.001G054600.1 288 AWHAYTTKTIFTVYYKPRTSPAEFIVPFDQYMESMKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPKKWKDSKWRCLK 370
                         79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019368.11E-41156291IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.2E-41158277IPR015300DNA-binding pseudobarrel domain
CDDcd100177.90E-22160262No hitNo description
SMARTSM010192.0E-23162264IPR003340B3 DNA binding domain
PfamPF023621.2E-21162263IPR003340B3 DNA binding domain
PROSITE profilePS5086312.012162264IPR003340B3 DNA binding domain
PfamPF065073.9E-36288370IPR010525Auxin response factor
PfamPF023091.5E-12725822IPR033389AUX/IAA domain
SuperFamilySSF542778.34E-13731817No hitNo description
PROSITE profilePS5174524.519737821IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 861 aa     Download sequence    Send to blast
MTNTEVAMKG NCVNGRGGGE SFSSGYSEPK DGRNTVEGQN GHSTNQAPAI DPETALYNEL  60
WHACAGPLVT VPREQDRVFY FPQGHIEQVE ASTSQVADEQ MPVYNLPSKI LCRVINVQLK  120
AEPDTDEVFA QVTLLPEPNQ DENTVNKEPP APQPPRFHVH SFCKTLTASD TSTHGGFSVL  180
RRHADECLPP LDMSRQPPTQ ELVAKDLHGN EWRFRHIFRG QPRRHLLQSG WSVFVSSKRL  240
VAGDAFIFLR GENGELRVGV RRAMRQQGNV PSSVISSHSM HLGVLATAWH AYTTKTIFTV  300
YYKPRTSPAE FIVPFDQYME SMKNNYSIGM RFKMRFEGEE APEQRFTGTI VGIEDADPKK  360
WKDSKWRCLK VRWDETSTIP RPERVSPWKI EPALAPPALN PLPMPRPKRP RSNAVPSSPD  420
SSVLTREGSS KAIVDPSPAT GFSRVLQGQE FSTLRGNFGE SHESDTAEKS VIWRPTVDDE  480
KIDVVPTSRR FGSENWMSSG RHEPAAYADL LSGFRSNADS SLGYCPPLVD QTSLAGNPMR  540
RQLLDQEGKL GSWSLMSSGL SLKLVDSNAK PSVQGSEVPY QARGNGRFSG FGEYPVLQGH  600
RIEHPHGNWL MPPPTSSNYE NPIQSRDLMP KASLGQDHEN GKSREGSCKL FGIPLISNSV  660
ASEPTVSPIN ATNKAASHVE AAPNQARTFT FDQKSEQPKF SPLAENLSIF NEQEKSFQPG  720
QPHTREVQSK SPSASTRSCT KVLMQGSALG RSVDLTKFNN YDELIAELDQ LFEFGGELMA  780
PKKNWLVVYT DDEGDMMLVG DDPWQEFCTM VRKIGIYTRE EVQKMKPGSL NSKGEDNLVS  840
AEGLDAKDVK CTSASSTENC *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1805539218354Auxin response factor 1
4ldw_A1e-1805539218354Auxin response factor 1
4ldw_B1e-1805539218354Auxin response factor 1
4ldx_A1e-1805539218354Auxin response factor 1
4ldx_B1e-1805539218354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gra.16890.0flower|seedling| flowering
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone. Expressed in developing siliques. {ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078, ECO:0000269|PubMed:15960614}.
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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012467386.10.0PREDICTED: auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A0D2PM560.0A0A0D2PM56_GOSRA; Auxin response factor
STRINGGorai.001G054600.10.0(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. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  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. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  4. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  5. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  6. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  7. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  8. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  9. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  10. 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]
  11. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  12. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  13. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  14. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]
  15. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]