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 Sobic.003G411900.1.p
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family ARF
Protein Properties Length: 811aa    MW: 90774.6 Da    PI: 6.4214
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.003G411900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.33e-23128229199
                           EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS
                    B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 
                           f+k+lt sd++++g +++ +++a+e+       +++++  ++l+ +d++g +W++++i+r++++r++l++GW+ Fv++++L +gD ++F
  Sobic.003G411900.1.p 128 FCKTLTASDTSTHGGFSVLRRHADEClppldmtQSPPT--QELVAKDLHGMEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIF 214
                           99*****************************7555544..58*********************************************** PP

                           EE-SSSEE..EEEEE-S CS
                    B3  83 kldgrsefelvvkvfrk 99 
                              + +++el+v+v+r+
  Sobic.003G411900.1.p 215 L--RGENGELRVGVRRA 229
                           *..449999*****996 PP
2Auxin_resp112.54e-37254335183
            Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                           a+ha++tks+F+v+Y+Pr+s+seF+++++++++++k+++s+GmRf+m+fe+e+++e+r++Gt+vg ++ldp  Wp+S Wr Lk
  Sobic.003G411900.1.p 254 AWHAINTKSMFTVYYKPRTSPSEFIIPYDQYMESVKNNYSIGMRFRMRFEGEEAPEQRFTGTIVGCENLDP-LWPDSSWRYLK 335
                           89*********************************************************************.9*******996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.9E-41117243IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.29E-39123257IPR015300DNA-binding pseudobarrel domain
CDDcd100173.89E-21126228No hitNo description
PfamPF023624.0E-21128229IPR003340B3 DNA binding domain
PROSITE profilePS5086311.928128230IPR003340B3 DNA binding domain
SMARTSM010191.8E-23128230IPR003340B3 DNA binding domain
PfamPF065071.4E-33254335IPR010525Auxin response factor
PfamPF023094.6E-6677734IPR033389AUX/IAA domain
SuperFamilySSF542774.81E-13692775No hitNo description
PROSITE profilePS5174524.764698791IPR000270PB1 domain
PfamPF023097.0E-8743783IPR033389AUX/IAA 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: 811 aa     Download sequence    Send to blast
MPPAAAMALP SQAPSNSGDP LYPELWRACA GPLVTVPRVG DLVFYFPQGH IEQVEASMNQ  60
VAGNQMRLYD LPSKLLCRVL NVELKAETDT DEVYAQIMLM PEPEQTDVAA EKASSASAAS  120
PRPAVRSFCK TLTASDTSTH GGFSVLRRHA DECLPPLDMT QSPPTQELVA KDLHGMEWRF  180
RHIFRGQPRR HLLQSGWSVF VSSKRLVAGD AFIFLRGENG ELRVGVRRAM RQLSNVPSSV  240
ISSQSMHLGV LATAWHAINT KSMFTVYYKP RTSPSEFIIP YDQYMESVKN NYSIGMRFRM  300
RFEGEEAPEQ RFTGTIVGCE NLDPLWPDSS WRYLKVRWDE PSTIPRPDRV SPWKIEPASS  360
PPVNPLPLSS RVKRPRQNAP PPSPEASVLT KESAAKIDID SAQTQHQNSV LQGQEQMTLR  420
NNLTESNDSD STVQKPMMWS PSPNGKAHTN FQQRPAMDSW MPMGRRETDF KDSRSAFKDA  480
RTASQSFRDT QGFFMQAYDD NHHRLSFNNQ FQDQGSAHRF ADPYFYMAQQ PSLTVESSTR  540
TQTANNDLRF WGDQNSIYGN PGDQQQQGFS FGQNPSSWLN QPFPQVEQPR VVRPHATVAP  600
FDLEKTREGS GFKIFGFQVD TTSPSPAQLS SPLCAIREHV VQTRPSAPVN ELQPVQNECL  660
PEGSVSTAGT ATENEKNIQQ AQPSSKDIQS KSQGASTRSC TKVHKQGVAL GRSVDLSKFT  720
DYDELKAELD KMFEFNGELV SANRSWQIVY TDNEGDMMLV GDDPWEEFCS IVRKIYIYTK  780
EEVQKMNSKS SAPRKEEPLT VGEGCAATNE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1651936017357Auxin response factor 1
4ldw_A1e-1651936017357Auxin response factor 1
4ldw_B1e-1651936017357Auxin response factor 1
4ldx_A1e-1651936017357Auxin response factor 1
4ldx_B1e-1651936017357Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.38720.0callus| embryo| leaf| ovary| panicle
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
MP00574DAPTransfer from AT5G62000Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.003G411900.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0676050.0BT067605.1 Zea mays full-length cDNA clone ZM_BFc0099C24 mRNA, complete cds.
GenBankKJ7268150.0KJ726815.1 Zea mays clone pUT3354 ARF transcription factor (ARF25) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021311466.10.0auxin response factor 4
SwissprotQ5JK200.0ARFD_ORYSJ; Auxin response factor 4
TrEMBLA0A1B6Q7Z00.0A0A1B6Q7Z0_SORBI; Auxin response factor
STRINGSi000340m0.0(Setaria italica)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP117836111
Representative plantOGRP5501582
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. 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. Song X, et al.
    Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
    Plant J., 2012. 71(3): p. 378-89
    [PMID:22443269]
  3. Kishimoto N, et al.
    Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions.
    Theor. Appl. Genet., 1994. 88(6-7): p. 722-6
    [PMID:24186168]