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 PGSC0003DMP400016579
Common NameLOC102588795
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: 496aa    MW: 54537.9 Da    PI: 8.8487
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400016579genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.64.5e-055676323
                          ETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                          C++Cgk F r  nL+ H r H
  PGSC0003DMP400016579 56 CEICGKGFQRDQNLQLHRRGH 76
                          *******************88 PP
2zf-C2H213.40.00023130152123
                           EEETTTTEEESSHHHHHHHHHHT CS
               zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                           +kC++C+k++  +s+ k H +t+
  PGSC0003DMP400016579 130 WKCEKCSKRYAVQSDWKAHSKTC 152
                           58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.604.3E-55376IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.91E-65376No hitNo description
SMARTSM003550.0765476IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.4895476IPR007087Zinc finger, C2H2
PROSITE patternPS0002805676IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.6E-5118151IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.91E-6125150No hitNo description
SMARTSM00355130130150IPR015880Zinc finger, C2H2-like
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: 496 aa     Download sequence    Send to blast
MTDEVISNGF THDNSIEGSN PPPLKKKRNL PGNPDPEAEV IALSPKTLMA TNRFLCEICG  60
KGFQRDQNLQ LHRRGHNLPW KLKQRTSKEV RKRVYVCPEK ACVHHHPSRA LGDLTGIKKH  120
YCRKHGEKKW KCEKCSKRYA VQSDWKAHSK TCGTREYRCD CGTIFSRRDS FVTHRAFCDA  180
LAEETARVTA ASNMHNPLAM ENNINYHFIG APLGPNMAQH FSSLFKPVSN NNENSDPLRR  240
DQLSLWNNIG VAQEQDQIGI NINNLREIHQ ISPLFHHTSP APTPVYDANA LLASRNSNAP  300
PVSYNNNHIN WDQFIGTKIS PINNAEQLSN TSSANISVPS LFSSQQQIAL SSSTANMSAT  360
ALLQKAAQIG ATTTTATDPS IFLGNFTMNN CNNNKNNDND NNKFCGFYVS TPTTNNSIST  420
SLGSDVDQSS SVNDFSATIH PIQMYPPSKR RHIQIEDSVK GVGGGAGSGA GGQTRDFLGV  480
GVQSICHPSS INGWI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-36126193370Zinc finger protein JACKDAW
5b3h_F4e-36126193370Zinc finger protein JACKDAW
Search in ModeBase
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
PlantRegMapPGSC0003DMP400016579
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
GenBankHG9755190.0HG975519.1 Solanum lycopersicum chromosome ch07, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006348832.20.0PREDICTED: zinc finger protein NUTCRACKER
SwissprotQ9ZWA61e-157IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLM1AJS60.0M1AJS6_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000242720.0(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
AT1G03840.11e-136C2H2 family 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. 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]
  3. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]