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 Solyc06g072360.2.1
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: 393aa    MW: 44825.6 Da    PI: 9.0408
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc06g072360.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.79.6e-064870123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        y C++C++ F r  nL+ H r+H
  Solyc06g072360.2.1 48 YICEICNQGFQRDQNLQMHRRRH 70
                        89********************9 PP
2zf-C2H216.81.9e-05125147123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         ++C++C+k +  +s++k H++t+
  Solyc06g072360.2.1 125 WVCEKCNKGYAVQSDYKAHLKTC 147
                         58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.22E-54770No hitNo description
Gene3DG3DSA:3.30.160.601.1E-54770IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00654870IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8664870IPR007087Zinc finger, C2H2
PROSITE patternPS01359050130IPR019786Zinc finger, PHD-type, conserved site
PROSITE patternPS0002805070IPR007087Zinc finger, C2H2
SMARTSM0035519089119IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.7E-4116146IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.22E-5120145No hitNo description
SMARTSM0035546125152IPR015880Zinc 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: 393 aa     Download sequence    Send to blast
MTSSEINENS CINNNNNNKR KRRPAGTPDP DAEVVSLSPK TLLESDRYIC EICNQGFQRD  60
QNLQMHRRRH KVPWKLLKRE TPIVKKRVFV CPEPTCLHHD PCHALGDLVG IKKHFRRKHS  120
NHKQWVCEKC NKGYAVQSDY KAHLKTCGTR GHSCDCGRVF SRVESFIEHQ DACSFGRLRS  180
ESQSLIQLPS APCLSRTASS PSPSSDHTNN LITTTNTIPW PNFIINTPNA MIKEHNLELQ  240
LLTTTSTTTT SPCSPFDVSI SSKSRDDHNL QLSIGSSDLS ENNNNDTHRW RNDVEGLRHA  300
LAEKVYAEET RKEARREIEL AEEELSNARR IRRQAQMELE KAQVLKEEAI RKINFTLSQI  360
TCYACKQKFQ PKKTTTTTTR TTSIDQNIHL KV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-17121173355Zinc finger protein JACKDAW
5b3h_F2e-17121173355Zinc 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc06g072360.2.1
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2401918e-06Solanum lycopersicum strain Heinz 1706 chromosome 1 clone hba-100n4 map 1, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004241469.10.0protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE31e-142IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3Q7H1Z40.0A0A3Q7H1Z4_SOLLC; Uncharacterized protein
STRINGSolyc06g072360.2.10.0(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
AT1G68130.11e-120indeterminate(ID)-domain 14
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]