PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID orange1.1g003580m
Common NameCISIN_1g003580mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family ARF
Protein Properties Length: 810aa    MW: 89728.5 Da    PI: 7.0458
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g003580mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.65.9e-24172273199
                        EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                        f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   +
  orange1.1g003580m 172 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyK-QQRPSQELVAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL--R 260
                        99****************************963.3445679************************************************..4 PP

                        SSEE..EEEEE-S CS
                 B3  87 rsefelvvkvfrk 99 
                         +++el+++++r+
  orange1.1g003580m 261 GKDGELRLGIRRS 273
                        499999****996 PP

2Auxin_resp121.18.5e-40298379182
         Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                        +a+a+stks+F+v+Y+Pra++++Fv++++k++k + +++++G+Rfkm+fe++ds+err+ G+v+g++dldp+rWpnSkWr+L
  orange1.1g003580m 298 VANAVSTKSMFHVFYSPRATHADFVIPYQKYVKIIMNPICIGTRFKMRFEMDDSPERRCNGVVTGITDLDPYRWPNSKWRCL 379
                        689******************************************************************************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.07E-43164287IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-40165283IPR015300DNA-binding pseudobarrel domain
CDDcd100176.24E-23170272No hitNo description
SMARTSM010191.0E-23172274IPR003340B3 DNA binding domain
PfamPF023624.9E-22172273IPR003340B3 DNA binding domain
PROSITE profilePS5086312.999172274IPR003340B3 DNA binding domain
PfamPF065071.6E-33298379IPR010525Auxin response factor
SuperFamilySSF542771.18E-7675748No hitNo description
PROSITE profilePS5174518.034679762IPR000270PB1 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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 810 aa     Download sequence    Send to blast
MEFDLNHAAT TEGEKIAFCN GDCGKNNSGC VCYLNSSSSS SSCSANSSSS SSLSSSIYFE  60
LWHACAGPLT SLPKKGNVVV YFPQGHLEQV ASSSAFPPIE VPNFDLQPQI FCKVVDVQLL  120
ANKENDEVYT QVALLPQPEL EGLNLEAKQL EDLGVDEEGG GRSPTKSTPH MFCKTLTASD  180
TSTHGGFSVP RRAAEDCFPP LDYKQQRPSQ ELVAKDLHGV EWRFRHIYRG QPRRHLLTTG  240
WSIFVSQKNL VSGDAVLFLR GKDGELRLGI RRSVQPRNGL PDSILSKQNS YPNVLSVVAN  300
AVSTKSMFHV FYSPRATHAD FVIPYQKYVK IIMNPICIGT RFKMRFEMDD SPERRCNGVV  360
TGITDLDPYR WPNSKWRCLM VRWDECIGSD HQEQVSPWEI DRSVSLPPLS IQSSPRMKKL  420
RTGLQAPPPD YPVSARGGGV LDFEESVRSS KVLQGQENVG FVSPLYGCDT VNHPLGFEMR  480
APAHQSLALN GIRKDNINEL VRALPTSYTG FVESNRFPKV LQGQEICPLR SLTGKVDLNL  540
GTWGKPNFGC NSMNMYQASK PNIYPPPSES LSNMFFPYGD MPKTVQHHTM PPYASNLQRE  600
NVKLNSSSIQ MPAIGAEIRK ANLLNEHKPV ENIPTPTFKA NMRSHKDGSF NGTAAGCKLF  660
GFSLTSETPT PSSQSPGKRS CTKVHKQGSL VGRAIDLWRL NGYNDLLSEL EHLFNMEGLL  720
RDPAKGWRIL YTDSENDVMV VGDDPWHSEF CNEVSKIHIY TQEEVEKMTI GTTDDTQSCL  780
DQAPVIMEVS VSKSSSVSQP DSSPTVVRV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1175340115353Auxin response factor 1
4ldw_A1e-1175340115353Auxin response factor 1
4ldw_B1e-1175340115353Auxin response factor 1
4ldy_A1e-1175340115353Auxin response factor 1
4ldy_B1e-1175340115353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.179370.0flower
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
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. {ECO:0000269|PubMed:12036261}.
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_006488135.10.0auxin response factor 4 isoform X1
RefseqXP_024035237.10.0auxin response factor 4 isoform X1
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A067GCK90.0A0A067GCK9_CITSI; Auxin response factor
STRINGXP_006488135.10.0(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
Publications ? help Back to Top
  1. 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]
  2. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  3. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  4. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. 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]