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 Lj4g3v2401010.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family C2H2
Protein Properties Length: 421aa    MW: 46945.5 Da    PI: 8.183
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj4g3v2401010.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.74.9e-066082123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     y+C++C++ F r  nL+ H r+H
  Lj4g3v2401010.1 60 YVCEICNQGFQRDQNLQMHRRRH 82
                     9*********************9 PP
2zf-C2H2156.9e-05138160123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      ++C +C+k +  +s++k H +t+
  Lj4g3v2401010.1 138 WVCDKCNKGYAVQSDYKAHVKTC 160
                      58*******************98 PP
3zf-C2H2110.0013168186523
                      TTTEEESSHHHHHHHHHHT CS
          zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                      dCg++Fsr +++  H+ t+
  Lj4g3v2401010.1 168 DCGRVFSRVESFIEHQDTC 186
                      9***************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.7E-55982IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.36E-55982No hitNo description
PROSITE profilePS5015710.976082IPR007087Zinc finger, C2H2
SMARTSM003550.00526082IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806282IPR007087Zinc finger, C2H2
SMARTSM00355210102132IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.6E-4129159IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.36E-5133158No hitNo description
SMARTSM0035552138165IPR015880Zinc 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: 421 aa     Download sequence    Send to blast
MLDNTASSSG APSSSDIAAF ALSENGVLNN KRKRRPAGTP DPDAEVVSLS PKTLLESDRY  60
VCEICNQGFQ RDQNLQMHRR RHKVPWKLLK RETTQGQKKR VFVCPEPSCL HHDPCHALGD  120
LVGIKKHFRR KHSNHKQWVC DKCNKGYAVQ SDYKAHVKTC GTRGHSCDCG RVFSRVESFI  180
EHQDTCNMRL PRQELQALQP ACSSRTASST SPSNEANFSI APLQGLPLPK PPPADQPSTS  240
NTHNLELQLL SPSSTIPKEN RNPRENHNET RLKLSIGSCT NNDGHIGNEE SERNNNNNVV  300
GDNSIFEVAR LKEFAGEELK LAMAEKAYAE EARREAKRQI EIAEVEFENA KRIRKQAQAE  360
LGKAEDLRKQ AMKKISSTVM EITCQACKQQ FQNSTVASDQ ETSIVVSYVS SANTEGEAAE  420
E
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-17136187556Zinc finger protein JACKDAW
5b3h_F1e-17136187556Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Lja.54790.0cell culture| floral bud
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
PlantRegMapLj4g3v2401010.1
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT1382190.0BT138219.1 Lotus japonicus clone JCVI-FLLj-22L13 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006580086.10.0protein SHOOT GRAVITROPISM 5 isoform X1
RefseqXP_028232544.10.0zinc finger protein SHOOT GRAVITROPISM 5-like isoform X1
SwissprotF4IPE31e-159IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLI3SCM20.0I3SCM2_LOTJA; Uncharacterized protein
STRINGGLYMA05G26780.20.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF17693289
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G68130.11e-111indeterminate(ID)-domain 14
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. 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]
  3. 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]
  4. 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]
  5. 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]