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 Solyc07g053570.2.1
Common NameLOC101254916
Organism
Solanum lycopersicum
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; Lycopersicon
Family C2H2
Protein Properties Length: 503aa    MW: 55280.8 Da    PI: 8.9851
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc07g053570.2.1genomeITAGView 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
  Solyc07g053570.2.1 56 CEICGKGFQRDQNLQLHRRGH 76
                        *******************88 PP
2zf-C2H212.70.00037130152123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC +C+k++  +s+ k H +t+
  Solyc07g053570.2.1 130 WKCDKCSKRYAVQSDWKAHSKTC 152
                         58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.604.4E-55376IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.74E-65376No hitNo description
SMARTSM003550.0765476IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.4895476IPR007087Zinc finger, C2H2
PROSITE patternPS0002805676IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.3E-5118151IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.74E-6125150No hitNo description
SMARTSM00355140130150IPR015880Zinc 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: 503 aa     Download sequence    Send to blast
MTEEVISNGF THDNSIEGSN PPPLKKKRNL PGNPDPEAEV IALSPKTLMA TNRFLCEICG  60
KGFQRDQNLQ LHRRGHNLPW KLKQRTSKEV RKRVYVCPEK VCVHHHPSRA LGDLTGIKKH  120
YCRKHGEKKW KCDKCSKRYA VQSDWKAHSK TCGTREYRCD CGTIFSRRDS FVTHRAFCDA  180
LAEETARVTA ASNMHNPLAM ANNINYHFIG APLGPNMAQH FSSLFKPVSN NNNNNNNNEN  240
SDPMRRNQLS LWNNIGVAQE QDQIGININN LREIHQINPL LHHTSAPAPA PVYDANTLLA  300
SSRSNAPPVS YNNNNHINWD QFIGSKTSPI NNAEQLSNTS SANISVPSLF SCQQQIALSS  360
PSANMSATAL LQKAAQIGAT TTTDPSIFLG NFSMNNCSNN NNNKNNDNNK FCGFYVSTPT  420
TNNSISNSLG SDVDQSSSVN DFSATIHPIQ MYPPPKRRHI QIEDSVKGVE VGAGGGAGGQ  480
TRDFLGVGVQ SICHPSSING LI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-35126193370Zinc finger protein JACKDAW
5b3h_F1e-35126193370Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
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}.
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
PlantRegMapSolyc07g053570.2.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004243388.10.0zinc finger protein NUTCRACKER
SwissprotQ9ZWA61e-153IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A3Q7HF560.0A0A3Q7HF56_SOLLC; Uncharacterized protein
STRINGSolyc07g053570.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10324350
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.11e-132C2H2 family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  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]