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 Pp3c6_26890V3.1.p
Common NameARF
Organism
Physcomitrella patens
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
Family ARF
Protein Properties Length: 715aa    MW: 77564.9 Da    PI: 6.9804
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c6_26890V3.1.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B372.84.3e-23136237199
                        EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                        f k+lt+sd+++ g +++p+ +ae++         ++ +  t+  +d +g++W++++iyr++++r++lt+GW+ Fv++++L +gD +vF ++
  Pp3c6_26890V3.1.p 136 FAKTLTQSDANNGGGFSIPRYCAETIfppldycIDPPVQ--TVLAKDVHGEVWKFRHIYRGTPRRHLLTTGWSTFVNQKKLVAGDAIVFLRI 225
                        89****************************997444445..89***********************************************54 PP

                        SSSEE..EEEEE-S CS
                 B3  86 grsefelvvkvfrk 99 
                           ++el+v+v+r+
  Pp3c6_26890V3.1.p 226 --ASGELCVGVRRS 237
                        ..68999****985 PP
2Auxin_resp101.88.9e-34319401283
         Auxin_resp   2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                        a  a +++ FevvY+Prast+eF+vk+  v++al++++ +GmRfkmafetedss++++ +Gt+++v+++dpv Wp S+Wr+L+
  Pp3c6_26890V3.1.p 319 AALAVSGERFEVVYYPRASTAEFCVKAGLVKRALEQSWYAGMRFKMAFETEDSSRISWfMGTIAAVQAADPVLWPSSPWRVLQ 401
                        66788999*************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.5E-35129247IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.14E-29129254IPR015300DNA-binding pseudobarrel domain
CDDcd100179.18E-22135236No hitNo description
PROSITE profilePS5086312.252136238IPR003340B3 DNA binding domain
SMARTSM010199.0E-22136238IPR003340B3 DNA binding domain
PfamPF023626.8E-21136237IPR003340B3 DNA binding domain
PfamPF065073.6E-30318401IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009734Biological Processauxin-activated signaling pathway
GO:0048829Biological Processroot cap development
GO:0051301Biological Processcell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 715 aa     Download sequence    Send to blast
MPGPVPLLSM SVKSESLDDI GGHEKKSVTG SEVGGLDAQL WHACAGGMVQ LPHVGAKVVY  60
FPQGHGEQAA STPEFPRTLV PNGSVPCRVV SVNFLADTET DEVFARICLQ PEIGSSAQDL  120
TDDSLASPPL EKPASFAKTL TQSDANNGGG FSIPRYCAET IFPPLDYCID PPVQTVLAKD  180
VHGEVWKFRH IYRGTPRRHL LTTGWSTFVN QKKLVAGDAI VFLRIASGEL CVGVRRSMRG  240
VSNGESSSWH SSISNASTIR PSRWEVKGTE SFSDFLGGVG DNGYALNSSI RSENQGSPTT  300
SSFARDRARV TAKSVLEAAA LAVSGERFEV VYYPRASTAE FCVKAGLVKR ALEQSWYAGM  360
RFKMAFETED SSRISWFMGT IAAVQAADPV LWPSSPWRVL QVTWDEPDLL QGVNRVSPWQ  420
LELVATLPMQ LPPVSLPKKK LRTVQPQELP LQPPGLLSLP LAGTSNFGGH LATPWGSSVL  480
LDDASVGMQG ARHDQFNGLP TVDFRNSNYK RPREFSRDNQ YQIQDHQVFH PRPVLNEPPA  540
TNTGNYFSLL PSLQRRPDIS PSIQPLAFMS ASGSSQLETS STKTAATSFF LFGQFIDPSC  600
TSKPQQRSTV INNASVAGDG KHPGTNNSSS DNKSEDKDNC RDVQPILNGI AVRSGFRADI  660
AAKKFQQSDS AHPTEASRGS QVSSLPWWQT QDAHKDQEFH GDSQTPHTPA SGSQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A2e-763542218353Auxin response factor 1
4ldw_A2e-763542218353Auxin response factor 1
4ldw_B2e-763542218353Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1436442PKKKLRT
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ppa.22610.0protonema
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269|PubMed:17408882}.
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).
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00461DAPTransfer from AT4G30080Download
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_024377979.10.0auxin response factor 16-like
RefseqXP_024377980.10.0auxin response factor 16-like
RefseqXP_024377981.10.0auxin response factor 16-like
RefseqXP_024377982.10.0auxin response factor 16-like
RefseqXP_024377983.10.0auxin response factor 16-like
RefseqXP_024377985.10.0auxin response factor 16-like
RefseqXP_024377986.10.0auxin response factor 16-like
RefseqXP_024377987.10.0auxin response factor 16-like
RefseqXP_024377988.10.0auxin response factor 16-like
SwissprotQ653H71e-162ARFR_ORYSJ; Auxin response factor 18
TrEMBLA0A2K1KHA00.0A0A2K1KHA0_PHYPA; Auxin response factor
STRINGPP1S279_9V6.10.0(Physcomitrella patens)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5261578
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G30080.11e-154auxin response factor 16
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Khraiwesh B, et al.
    Transcriptional control of gene expression by microRNAs.
    Cell, 2010. 140(1): p. 111-22
    [PMID:20085706]
  3. Huang J,Li Z,Zhao D
    Deregulation of the OsmiR160 Target Gene OsARF18 Causes Growth and Developmental Defects with an Alteration of Auxin Signaling in Rice.
    Sci Rep, 2016. 6: p. 29938
    [PMID:27444058]