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 Carubv10004220m
Common NameCARUB_v10004220mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family ARF
Protein Properties Length: 745aa    MW: 82616.2 Da    PI: 8.4962
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10004220mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.12e-24194295199
                      EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                      f k+lt+sd+++ g +++p+ +ae++        +++ +  t+  +d +g +W++++iyr++++r++lt+GW++Fv++++L +gD++vF+  + 
  Carubv10004220m 194 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RA 283
                      89****************************985444444..8999*********************************************..44 PP

                      SEE..EEEEE-S CS
               B3  88 sefelvvkvfrk 99 
                      +++ l+v+++r+
  Carubv10004220m 284 ENGDLCVGIRRA 295
                      88999****997 PP
2Auxin_resp113.52e-37353436183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                      aa+ a ++ +FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  Carubv10004220m 353 AATLAISGRPFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVNVSDPIRWPNSPWRLLQ 436
                      67788899**************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.5E-39186301IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019369.03E-30189297IPR015300DNA-binding pseudobarrel domain
CDDcd100175.89E-22192294No hitNo description
SMARTSM010197.1E-23194296IPR003340B3 DNA binding domain
PfamPF023622.1E-22194295IPR003340B3 DNA binding domain
PROSITE profilePS5086313.352194296IPR003340B3 DNA binding domain
PfamPF065073.1E-31353436IPR010525Auxin response factor
PROSITE profilePS5174517.488658738IPR000270PB1 domain
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
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 745 aa     Download sequence    Send to blast
MAEEPKAVSF IYTNSFFPIF LCAKVKKLPY PILKQQNQLR NLQILTKPRL VFFLNLRSFV  60
QICHCFSKTG VKKKMINVMN PLKGGSEKGL DPQLWHACAG GMVRMPPMNS KVFYFPQGHA  120
ENAYDCVDFG NMPIHPMVLC RVLAIKYMAD AESDEVFAKL RLIPLKEDDY VDHEYTDGDD  180
SNGFESNSEK TPSFAKTLTQ SDANNGGGFS VPRYCAETIF PRLDYNAEPP VQTILAKDVH  240
GDVWKFRHIY RGTPRRHLLT TGWSNFVNQK KLVAGDSIVF MRAENGDLCV GIRRAKRGGI  300
GNGPEYSAGW NPIGGSCGYS SLLREDESNT LRRSNCSLAD RKGKVTAESV IEAATLAISG  360
RPFEVVYYPR ASTSEFCVKA LDARAAMRIP WCSGMRFKMA FETEDSSRIS WFMGTVSAVN  420
VSDPIRWPNS PWRLLQVAWD EPDLLQNVKR VNPWLVELVS NVHPIPLTSF SPPRKKMRLP  480
QHPDYNNLIN SIPIPSFPSN PLIRSSPLSS VLDNVPVGLQ GARHNAHQYY GLSSSDLHHY  540
YLNRPPPPPP SSLPLSPSLG LRNIDSKNEK GFCFLTMGTT PCNDTASKKS HIVLFGKLIL  600
PEEQLSEKGS TDTANVEKTQ ISSGGSNQNN GIAGRDLSSS DEGSPCSKKV HDASGLETGH  660
CKVFMESDEV GRTLDLSVLG SYDELSRKLS DMFGIKKSEM LSSVLYKDAS GAIKYPGNEP  720
FSEFLKTARR LTILTEQGSE SVVI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-757645737388Auxin response factor 5
Search in ModeBase
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00461DAPTransfer from AT4G30080Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10004220m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0597920.0AY059792.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023635190.10.0auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLR0GY890.0R0GY89_9BRAS; Auxin response factor
STRINGXP_006283190.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G30080.10.0auxin response factor 16
Publications ? help Back to Top
  1. Yang ZB, et al.
    TAA1-regulated local auxin biosynthesis in the root-apex transition zone mediates the aluminum-induced inhibition of root growth in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2889-904
    [PMID:25052716]
  2. Bennett T,van den Toorn A,Willemsen V,Scheres B
    Precise control of plant stem cell activity through parallel regulatory inputs.
    Development, 2014. 141(21): p. 4055-64
    [PMID:25256342]
  3. Zhang GZ, et al.
    Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana.
    Plant Mol. Biol., 2016. 90(1-2): p. 77-93
    [PMID:26496910]
  4. Ye Y, et al.
    Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination.
    Plant J., 2016. 85(1): p. 3-15
    [PMID:26611158]
  5. Liu Z, et al.
    Repression of callus initiation by the miRNA-directed interaction of auxin-cytokinin in Arabidopsis thaliana.
    Plant J., 2016. 87(4): p. 391-402
    [PMID:27189514]
  6. 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]
  7. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]
  8. Lin JS, et al.
    MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis.
    Front Plant Sci, 2018. 9: p. 68
    [PMID:29449855]