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 PGSC0003DMP400003130
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family C2H2
Protein Properties Length: 457aa    MW: 50760.2 Da    PI: 9.7748
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400003130genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.32.7e-055981123
                          EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                          + C++C+k F r  nL+ H r H
  PGSC0003DMP400003130 59 FICEICNKGFQRDQNLQLHRRGH 81
                          89*******************88 PP
2zf-C2H214.10.00014136158123
                           EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                           +kC++C+k +  +s+ k H +t+
  PGSC0003DMP400003130 136 WKCEKCSKKYAVQSDWKAHTKTC 158
                           58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.05E-75881No hitNo description
Gene3DG3DSA:3.30.160.601.2E-55881IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121715.4E-55981IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0225981IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8455981IPR007087Zinc finger, C2H2
PROSITE patternPS0002806181IPR007087Zinc finger, C2H2
SMARTSM00355100101131IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-4124157IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.05E-7131156No hitNo description
SMARTSM00355130136156IPR015880Zinc 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: 457 aa     Download sequence    Send to blast
MSGDLFSIHQ QQQQLLVEQN PNPKANSSSK KRRNLPGTPD PDAEVIAISP KTLMATNRFI  60
CEICNKGFQR DQNLQLHRRG HNLPWKLKQR NKQEIVKKKV YICPEKTCVH HDPSRALGDL  120
TGIKKHFSRK HGEKKWKCEK CSKKYAVQSD WKAHTKTCGT REYKCDCGTL FSRKDSFITH  180
RAFCDALAEE SARITSVGTT PNNLNFNQQQ QQPVGISQIG TSFVQDFTSM TTVNPLHQHQ  240
QKPRLSLWLN QPNNMSSPSS NLFGLPDHHM VQIPSPNMFG TASSIGNQIL TPTTTTTNTP  300
ATSNPPIPMS ATALLQKAAQ MGSTKSTPNY FSNTFGVMHS SSSPSSNNTT QIFNNNEIHQ  360
AFAKQTEDYN QTENILINGC PNMNLSVNSK AINLDQALLQ TGGMHNQTVH FNLHNSLTRD  420
FLGMGNEGGQ PFLPQELAKF ASMNAAMGLS HYSTGH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-38132197368Zinc finger protein JACKDAW
5b3h_F7e-38132197368Zinc 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
PlantRegMapPGSC0003DMP400003130
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754480.0HG975448.1 Solanum pennellii chromosome ch09, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006361805.20.0PREDICTED: zinc finger protein JACKDAW-like isoform X1
SwissprotQ700D21e-127IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLM0ZNC90.0M0ZNC9_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000043900.0(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10324350
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-103C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  3. 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]
  4. 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]
  5. 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]
  6. 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]