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 XP_009114218.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 449aa    MW: 50237.6 Da    PI: 8.698
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009114218.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.51.1e-0581103123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     y C++C++ F r  nL+ H r+H
  XP_009114218.1  81 YICEICNQGFQRDQNLQMHRRRH 103
                     89********************9 PP
2zf-C2H217.21.4e-05159181123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C+ C+ks+  +s++k H++t+
  XP_009114218.1 159 WVCERCSKSYAVQSDYKAHLKTC 181
                     58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.3E-580103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.54E-580103No hitNo description
SMARTSM003550.006581103IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.86681103IPR007087Zinc finger, C2H2
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355160123153IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-4150180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.54E-5154179No hitNo description
SMARTSM0035567159186IPR015880Zinc 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: 449 aa     Download sequence    Send to blast
MRTDQGAVVM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVTTTNTST QKRKRRPAGT  60
PDPDAEVVSL SPRTLLESDR YICEICNQGF QRDQNLQMHR RRHKVPWKLL KRDNNIEVKK  120
RVYVCPEPTC LHHAPCHALG DLVGIKKHFR RKHSNHKQWV CERCSKSYAV QSDYKAHLKT  180
CGTRGHSCDC GRVFSRVESF IEHQDNCSVR KVNREPPPPK TAVTVPACSS ITASTASTPS  240
SEGNNCGAVA VATPIPLEGR PIHLRNSCFT PSILTNSSSP NLELQLLPLT SNQNPNQENH  300
QHKVNEPSHH HHDTTNLNLS IAPSSSSYHR HYNNFDRIKE IMASEQMMKI AMKEKAYAEE  360
AKREAKRQRE MAENEFMNAK KIRQQAQAEL ERAKLLKEQS MKKISSMIMQ VTCQTCKGQF  420
QAVAVPAAAD ETSLVVSYMS SANTDGEES
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-18155207355Zinc finger protein JACKDAW
5b3h_F7e-18155207355Zinc 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
PlantRegMapXP_009114218.1
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_009114218.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
RefseqXP_013713043.10.0protein SHOOT GRAVITROPISM 5
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3P5YCK90.0A0A3P5YCK9_BRACM; Uncharacterized protein
STRINGBra017432.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G01940.10.0C2H2-like zinc finger protein
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]