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 LOC_Os01g13520.1
Common NameARF1, ARF16, LOC4327785, Os01g0236300, P0708G02.26
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family ARF
Protein Properties Length: 700aa    MW: 77502.4 Da    PI: 5.447
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g13520.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B369.64.2e-22122222198
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       f+k+ltpsd++++g +++ +++a+e+       +     +++l+ +d++g +W++k+iyr++++r++lt+GW+ Fv +++L +gD +v    +
  LOC_Os01g13520.1 122 FCKILTPSDTSTHGGFSVLRRHANEClppldmsMAT--PTQELITKDLHGSEWRFKHIYRGQPRRHLLTTGWSTFVTSKKLISGDAFVYL--R 210
                       99****************************974333..3458999******************************************999..4 PP

                       SSEE..EEEEE- CS
                B3  87 rsefelvvkvfr 98 
                       ++++e +v+v+r
  LOC_Os01g13520.1 211 SETGEQRVGVRR 222
                       477778999997 PP
2Auxin_resp96.92.9e-32248329183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a+ha++t+s+F v+Y+Pr s+s+++v+v+k+++a kv + vGmRfkm+fe+ed++ +++sGt+vg  d  +++W++S+W+sLk
  LOC_Os01g13520.1 248 ASHAIKTNSIFLVYYRPRLSQSQYIVSVNKYLAASKVGFNVGMRFKMSFEGEDVPVKKFSGTIVGEGD-LSLQWSGSEWKSLK 329
                       789*****************************************************************.566*********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.71E-37113251IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.6E-36114237IPR015300DNA-binding pseudobarrel domain
CDDcd100172.64E-16120222No hitNo description
SMARTSM010191.1E-16122224IPR003340B3 DNA binding domain
PfamPF023629.8E-20122222IPR003340B3 DNA binding domain
PROSITE profilePS5086311.138122224IPR003340B3 DNA binding domain
PfamPF065077.1E-29248329IPR010525Auxin response factor
PfamPF023093.9E-7581632IPR033389AUX/IAA domain
SuperFamilySSF542772.75E-9591668No hitNo description
PROSITE profilePS5174525.447595684IPR000270PB1 domain
Gene3DG3DSA:3.10.20.2401.6E-4597660No hitNo description
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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009071anatomyanther wall tapetum
PO:0001029developmental stageE tetrad stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 700 aa     Download sequence    Send to blast
MSSQGAGGGV GDPELFAELW RACAGPLVEV PQRDERVFYF LQGHLEQLQE PTDPALLAEQ  60
IKMFQVPYKI LCKVVNVELK AETETDEVFA QITLQPDPDQ ENLPTLPDPP LPEQPRPVVH  120
SFCKILTPSD TSTHGGFSVL RRHANECLPP LDMSMATPTQ ELITKDLHGS EWRFKHIYRG  180
QPRRHLLTTG WSTFVTSKKL ISGDAFVYLR SETGEQRVGV RRLVQKQSTM PASVISSQSM  240
HLGVLASASH AIKTNSIFLV YYRPRLSQSQ YIVSVNKYLA ASKVGFNVGM RFKMSFEGED  300
VPVKKFSGTI VGEGDLSLQW SGSEWKSLKV QWDEVTNVNG PERVSPWEIE TCDGTAPAIN  360
VPLQSATKNK RPREPSETID LQSLEPAQEF WLSGMPQQHE KTGIGSSEPN CISGHQVVWP  420
GEHPGYGAVS SSVCQNPLVL ESWLKDFNSS NKGVSPTLSE ISQKIFQVTS NEARIATWPA  480
RSAYQAEEPT SKLSSNTAAC GYRTEEVAPN ASKVVEGKKE PAMFRLFGVD LMKCTSISTT  540
TDDKSSVGAG EASAKGTGSH EDSGQLSAFS KVTKEHIAAD ESPQEIQSHQ NYTARTRIKV  600
QMHGNAVGRA VDLANLDGYE QLMNELEEMF NIKDLKQKWK VAFTDDEGDT MEVGDDPWLE  660
FCQMVRKIVL YPIEDEKKIE PHPKLLSSAN PEQDQKTGF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-15233507353Auxin response factor 1
4ldw_A1e-15233507353Auxin response factor 1
4ldw_B1e-15233507353Auxin response factor 1
4ldx_A1e-15233507353Auxin response factor 1
4ldx_B1e-15233507353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.222690.0callus| flower| leaf| panicle| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2139591530.0
Expression AtlasQ5NB85-
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).
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g13520.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin under light or dark conditions. {ECO:0000269|PubMed:17408882}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g13520
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1025210.0AK102521.1 Oryza sativa Japonica Group cDNA clone:J033095P08, full insert sequence.
GenBankEU8470080.0EU847008.1 Oryza sativa Japonica Group clone KCS385B05 auxin response factor mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015622434.10.0auxin response factor 1
SwissprotQ5NB850.0ARFA_ORYSJ; Auxin response factor 1
TrEMBLC6F1M30.0C6F1M3_ORYSJ; Auxin response factor
STRINGOS01T0236300-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP108236116
Representative plantOGRP1421044
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G59750.30.0auxin response factor 1
Publications ? help Back to Top
  1. Sato Y, et al.
    Auxin response factor family in rice.
    Genes Genet. Syst., 2001. 76(6): p. 373-80
    [PMID:11922106]
  2. 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]
  3. Wang D, et al.
    Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa).
    Gene, 2007. 394(1-2): p. 13-24
    [PMID:17408882]