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 Potri.007G135000.1
Common NamePOPTR_0007s01380g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family C2H2
Protein Properties Length: 478aa    MW: 52064.5 Da    PI: 8.8464
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.007G135000.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.74.3e-056484323
                        ETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                        C++Cgk F r  nL+ H r H
  Potri.007G135000.1 64 CEICGKGFQRDQNLQLHRRGH 84
                        *******************88 PP
2zf-C2H213.50.00022138160123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k++  +s+ k H +t+
  Potri.007G135000.1 138 WKCEKCSKRYAVQSDWKAHSKTC 160
                         58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.58E-66184No hitNo description
Gene3DG3DSA:3.30.160.604.1E-56184IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.4896284IPR007087Zinc finger, C2H2
SMARTSM003550.0766284IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806484IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-4126159IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.58E-6133158No hitNo description
SMARTSM00355130138158IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010150Biological Processleaf senescence
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0048573Biological Processphotoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 478 aa     Download sequence    Send to blast
MSENIMAAEE AITSSYNGSV ENPVGGSNPP ALKKKRNLPG TPDPEAEVIA LSPKTLMATN  60
RFLCEICGKG FQRDQNLQLH RRGHNLPWKL KQRTNNEVRK RVYVCPEKTC VHHHPSRALG  120
DLTGIKKHFC RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYKCDCG TLFSRRDSFI  180
THRAFCDALA EETARVNAVS SIRNLTAGNI SYHLPGNPLG PNMAQHFSSI FKPISSNDHH  240
TRQGGLSLWM HQGGVPHVSE AMGNNIQEIH QIGAMTSSGA IFGDPLAVSC SSTPPSDHYQ  300
LNWPVFGNKI SSNNAHEELT STLVLPLSNV KEAAAASQLV SVPSLYSTQQ QQSHQTTSAN  360
MSATALLQKA TQIGATSTDP SFLGSFGLKS FSTKAQDGNN KFCGLYGSSP ISTNPASDME  420
NSGNDEIPTL NQLQMYSAKR QKIFQSDQDS PAGGQTRDFL GVGVQAICHP SSINGWI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-37134200369Zinc finger protein JACKDAW
5b3h_F9e-37134200369Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed throughout development. {ECO:0000269|PubMed:21265895}.
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
UniprotTISSUE SPECIFICITY: Highly expressed in vegetative organs and at lower levels in flowers and siliques. Expressed predominantly in roots. In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:21265895, ECO:0000269|PubMed:25829440, ECO:0000305|PubMed:21265895}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that binds to the DNA sequence 5'-CTTTTGTCC-3' (PubMed:21265895, PubMed:25929516). Regulates photoperiodic flowering by modulating sugar transport and metabolism (PubMed:21265895, PubMed:25929516). Regulates SUS1 and SUS4 (PubMed:21265895). Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:25829440). {ECO:0000269|PubMed:21265895, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:25929516}.
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
PlantRegMapPotri.007G135000.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by 'SHORT-ROOT' (SHR)(PubMed:16640459). Strongly down-regulated by sugar deprivation, but not regulated by day-length. {ECO:0000269|PubMed:16640459}.
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006380280.10.0zinc finger protein NUTCRACKER
SwissprotQ9FFH31e-154IDD8_ARATH; Zinc finger protein NUTCRACKER
SwissprotQ9ZWA61e-154IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLU5G9H10.0U5G9H1_POPTR; Uncharacterized protein
STRINGPOPTR_0007s01380.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF46262951
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.11e-150C2H2 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]
  3. 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]