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_02596.1_g00004.1
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: 497aa    MW: 55289.8 Da    PI: 8.391
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02596.1_g00004.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.64.5e-057191323
                             ETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                             C++Cgk F r  nL+ H r H
  Rsa1.0_02596.1_g00004.1 71 CEICGKGFQRDQNLQLHRRGH 91
                             *******************88 PP
2zf-C2H213.20.00027145167123
                              EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                              +kC++C+k++  +s+ k H +t+
  Rsa1.0_02596.1_g00004.1 145 WKCGKCSKRYAVQSDWKAHSKTC 167
                              58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.18E-66891No hitNo description
Gene3DG3DSA:3.30.160.604.3E-56891IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.4896991IPR007087Zinc finger, C2H2
PROSITE patternPS0002807191IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.9E-4133166IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.18E-6140165No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 497 aa     Download sequence    Send to blast
MTAEEQTIIS SSGGYVQSLS ATDHVDHRHE PEPFNPPLAK RKRNLPGNPD PEAEVIALSP  60
KTLMATNRFL CEICGKGFQR DQNLQLHRRG HNLPWKLKQR TSKEIRKRVY VCPERSCVHH  120
NPTRALGDLT GIKKHFCRKH GEKKWKCGKC SKRYAVQSDW KAHSKTCGTR EYRCDCGTIF  180
SRRDSFITHR AFCDALAEET ARLNAASHLK SLTGNNLNYH YLMGTLIPSP QSPQSPPPSF  240
PFGAPQHHHH HFPITTTTTF DQLHHQDAMK PASSLSLWMG GNVNHHQVSN EDCTQPQSPQ  300
EDYNWVFGNA NNSGELSDSL ITHENINNFA HNENANAVTS LSVPSLFSNV DQIRQDANAA  360
VAAVANMSAT ALLQKAAQMG ATSSTPTITN DQSAFLQNFT SKISDQRQIV EDGGSDKFFA  420
LFGSNSVGLM SNNGLDHETL NPRNSVTVVS RIDELQNYPL KRRRVENGDV LEGGQTRDFL  480
GVGVQTMCRS SSINGWI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-35141208370Zinc finger protein JACKDAW
5b3h_F9e-35141208370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1460464KRRRV
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02596.1_g00004.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1895090.0AC189509.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB089B13, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018490519.10.0PREDICTED: zinc finger protein MAGPIE-like
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A0D3DZ450.0A0A0D3DZ45_BRAOL; Uncharacterized protein
STRINGBo8g115920.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.10.0C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]