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 Rsa1.0_00089.1_g00060.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 413aa    MW: 46445.2 Da    PI: 9.067
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00089.1_g00060.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.74.8e-066991123
                             EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                             y+C++C++ F r  nL+ H r+H
  Rsa1.0_00089.1_g00060.1 69 YVCEICNQGFQRDQNLQMHRRRH 91
                             9*********************9 PP
2zf-C2H213.80.00018148169223
                              EETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                               C+ C+k +  +s++k H++t+
  Rsa1.0_00089.1_g00060.1 148 ICERCSKGYAVQSDYKAHLKTC 169
                              7*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.98E-56692No hitNo description
Gene3DG3DSA:3.30.160.601.6E-56891IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00526991IPR015880Zinc finger, C2H2-like
PfamPF128740.026987No hitNo description
PROSITE profilePS5015710.976991IPR007087Zinc finger, C2H2
PROSITE patternPS0002807191IPR007087Zinc finger, C2H2
SMARTSM00355160111141IPR015880Zinc finger, C2H2-like
SMARTSM00355110147174IPR015880Zinc finger, C2H2-like
PfamPF095963.0E-5184224IPR019082Neurogenic mastermind-like, N-terminal
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0007219Biological ProcessNotch signaling pathway
GO:0009630Biological Processgravitropism
GO:0009965Biological Processleaf morphogenesis
GO:0010601Biological Processpositive regulation of auxin biosynthetic process
GO:0045944Biological Processpositive regulation of transcription from RNA polymerase II promoter
GO:0048444Biological Processfloral organ morphogenesis
GO:2000012Biological Processregulation of auxin polar transport
GO:2000904Biological Processregulation of starch metabolic process
GO:0016607Cellular Componentnuclear speck
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003713Molecular Functiontranscription coactivator activity
GO:0043621Molecular Functionprotein self-association
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 413 aa     Download sequence    Send to blast
MIDYERSNNT KNINHHQNPH PSSSSSGLLP DGNEAAVTQK RKRRPAGTPD PEAEVVSLSP  60
RTLLESDRYV CEICNQGFQR DQNLQMHRRR HKVPWKLLKR ETNEEVKKRV YVCPEPTCLH  120
HNPCHALGDL VGIKKHFRRK HSNHKQWICE RCSKGYAVQS DYKAHLKTCG TRGHSCDCGR  180
VFSRVESFIE HQDNCTMRQT QTSSHRLKQQ QQHTSNAKQT ALTSENIDLS IGPVLPRHPL  240
LRQSLPSDQQ PSGLLYPFVG ASATTGSGIE LQLLPSRVRA HDTSLSLSIG METTMSSYEK  300
GETSLLLGER EAAKRQIEIA ELEFAEAKRI RQHARGELHK AQLYREEASR RTSATIMQIT  360
CHDCKKYFQS VAASSPPPRL PQPPCTDEST SLAVSYVSSV ATEGEKASDR ASS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-17145195555Zinc finger protein JACKDAW
5b3h_F1e-17145195555Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor regulating starch metabolism by binding directly to the promoter of QQS (PubMed:21556057). The IDD14beta isoform attenuates the transcription factor activity by competitively forming heterodimers with reduced DNA-binding capacity(PubMed:21556057). Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Has a redundant role with IDD16 in directing leaf and floral organ morphogenesis (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:21556057, ECO:0000269|PubMed:24039602}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00089.1_g00060.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1894890.0AC189489.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB084K02, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018445099.10.0PREDICTED: protein indeterminate-domain 14-like
SwissprotQ9C9X70.0IDD14_ARATH; Protein indeterminate-domain 14
TrEMBLA0A078EZ840.0A0A078EZ84_BRANA; BnaA07g24790D protein
TrEMBLA0A397YPQ50.0A0A397YPQ5_BRACM; Uncharacterized protein
TrEMBLM4CIL60.0M4CIL6_BRARP; Uncharacterized protein
STRINGBra004050.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G68130.10.0indeterminate(ID)-domain 14
Publications ? help Back to Top
  1. Arendsee ZW,Li L,Wurtele ES
    Coming of age: orphan genes in plants.
    Trends Plant Sci., 2014. 19(11): p. 698-708
    [PMID:25151064]
  2. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]