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_03160.1_g00003.1
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: 507aa    MW: 55792.4 Da    PI: 10.1147
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03160.1_g00003.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.4e-0582104123
                              EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                              ++C++C+k F r  nL+ H r H
  Rsa1.0_03160.1_g00003.1  82 FVCEICNKGFQRDQNLQLHRRGH 104
                              89*******************88 PP
2zf-C2H215.74.3e-05159181123
                              EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                              ykC++C+k +  +s+ k H +t+
  Rsa1.0_03160.1_g00003.1 159 YKCEKCSKKYAVQSDWKAHAKTC 181
                              9*******************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.7E-581104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.75E-881104No hitNo description
SMARTSM003550.01782104IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.94982104IPR007087Zinc finger, C2H2
PfamPF121718.1E-582104IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SMARTSM0035578124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.6E-6147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.75E-8154179No hitNo description
SMARTSM0035574159179IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 507 aa     Download sequence    Send to blast
MHMIPGDPFS VSSSMGGFVH QEEHLRHLQQ HMPDLNPNSN TNPNAKPNSS SAKKKRNQPG  60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKEVIK  120
KKVYICPIKT CVHHDASRAL GDLTGIKKHY SRKHGEKKYK CEKCSKKYAV QSDWKAHAKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNPAISKTTT NLNFGNDTHF  240
MNNPNLPHGF VHRGVHHPDI NAAISQFGLG FGHDLSSMHA QGLSEMVQMA PAGSHHLFPL  300
SSSSSLPDFS GHHHNQQFQI PTTSTNSNLT LSSSQQTSAS LPSLQQQHQT PKDSSFSPLF  360
SSSSDNKQNK PLSPMSATAL LQKAAQMGST RSNSTTTPSI FAGATMTSSA SAGSHFPPRS  420
SSPMMIQQQL NTNVRRENHN FSPPISGVTT SSGDNNNQFQ SNGSGLNPAQ QMGLTRDFLG  480
VRNEHHPHQT GYRPFLPQEL ARFSPLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-41155222370Zinc finger protein JACKDAW
5b3h_F4e-41155222370Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03160.1_g00003.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018470362.10.0PREDICTED: zinc finger protein JACKDAW-like
SwissprotQ700D20.0IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A3P6D0B70.0A0A3P6D0B7_BRAOL; Uncharacterized protein
STRINGBo2g003880.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.10.0C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  2. Hirano Y, et al.
    Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
    Nat Plants, 2017. 3: p. 17010
    [PMID:28211915]
  3. Kobayashi A,Miura S,Kozaki A
    INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
    Plant Mol. Biol., 2017. 94(1-2): p. 1-13
    [PMID:28324206]
  4. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
    [PMID:28746306]
  5. Bustillo-Avendaño E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]