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 Solyc01g005060.2.1
Common NameLOC101262550
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: 340aa    MW: 38602.7 Da    PI: 8.5445
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g005060.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.89.4e-064870123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        y C +C++ F r  nL+ H r+H
  Solyc01g005060.2.1 48 YICDICDQGFQRDQNLQMHRRRH 70
                        89********************9 PP
2zf-C2H218.26.8e-06125146223
                         EETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                          C +Cgk +  +s++k H++t+
  Solyc01g005060.2.1 125 ICDKCGKAYAVQSDYKAHLKTC 146
                         7*******************98 PP
3zf-C2H210.70.0016154172523
                         TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                         dCg++Fsr +++  H+ ++
  Solyc01g005060.2.1 154 DCGRVFSRVESFIEHQDSC 172
                         9**************9887 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.609.2E-54770IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.94E-74770No hitNo description
PfamPF139121.2E-44771IPR007087Zinc finger, C2H2
SMARTSM003550.00734870IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.6994870IPR007087Zinc finger, C2H2
PROSITE patternPS01359050129IPR019786Zinc finger, PHD-type, conserved site
PROSITE patternPS0002805070IPR007087Zinc finger, C2H2
SMARTSM0035521088118IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-5115145IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.94E-7119144No hitNo description
SMARTSM0035541124151IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009590Biological Processdetection of gravity
GO:0009959Biological Processnegative gravitropism
GO:0009965Biological Processleaf morphogenesis
GO:0010031Biological Processcircumnutation
GO:0010601Biological Processpositive regulation of auxin biosynthetic process
GO:0048444Biological Processfloral organ morphogenesis
GO:2000012Biological Processregulation of auxin polar transport
GO:2000904Biological Processregulation of starch metabolic process
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 340 aa     Download sequence    Send to blast
MLDNSSSSEA LINSGDSNRR KRRPAGTPDP DAEVVSLSPK TLLESDRYIC DICDQGFQRD  60
QNLQMHRRRH KVPWKLVKRE IEVKKRVFVC PEPSCLHHDP CHALGDLVGI KKHFRRKHSD  120
NKQWICDKCG KAYAVQSDYK AHLKTCGTRG HSCDCGRVFS RVESFIEHQD SCTIRRIRPR  180
LQPITAACSS SDTNLPKLAI MPLPKNSTNL ELGLKSSSHH ENTIEEAHLK LSIGSSSPNH  240
EVLNLVMADK AYAEEARRNA KREMEYAERE FENAKRIRQQ AQAEIERAKQ LKEEAINRIS  300
SSILEITCHA CKNKFQTIDN NVDSSPPMSY MSSDGEREQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-17122172555Zinc finger protein JACKDAW
5b3h_F6e-17122172555Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
UniprotTISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00254DAPTransfer from AT2G01940Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc01g005060.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
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_004228757.10.0protein SHOOT GRAVITROPISM 5 isoform X2
SwissprotF4IPE31e-136IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3Q7E8970.0A0A3Q7E897_SOLLC; Uncharacterized protein
STRINGSolyc01g005060.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10222482
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G01940.11e-136C2H2-like zinc finger 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. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  4. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  5. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  6. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]