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_013607262.1
Organism
Brassica oleracea
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: 451aa    MW: 50478.8 Da    PI: 8.7847
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013607262.1genomeNCBIView 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_013607262.1  81 YICEICNQGFQRDQNLQMHRRRH 103
                     89********************9 PP
2zf-C2H214.50.0001159181123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C+ C+k +  +s++k H++t+
  XP_013607262.1 159 WVCERCSKGYAVQSDYKAHLKTC 181
                     58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.7E-578104No hitNo description
Gene3DG3DSA:3.30.160.601.3E-580103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.86681103IPR007087Zinc finger, C2H2
SMARTSM003550.006581103IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355160123153IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.7E-4150180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM00355100159186IPR015880Zinc 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: 451 aa     Download sequence    Send to blast
MRTDQGAVVM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVTTTNTST KKRKRRPAGT  60
PDPDAEVVSL SPRTLLESDR YICEICNQGF QRDQNLQMHR RRHKVPWKLL KRDNNIEVKK  120
RVYVCPEPTC LHHSPCHALG DLVGIKKHFR RKHSNHKQWV CERCSKGYAV QSDYKAHLKT  180
CGTRGHSCDC SRVFSRVESF IEHQDNCSVR KVNREPPPPQ TAVAVPACSS ITASTASTPS  240
SEGNNCGTVA VATHIPLEGR SIHLRNSCFT PSILTNASSL NLELQLLPLT SNQNPNQENH  300
QHKVNGPSHH HHHHDTTNLN LSIAPSSSSY HRHYNHFDRI KEIMASEQMM KIAMKEKAYA  360
EEAKREAKRQ REMAENEFMN AKKIRQQAQA ELERAKLLKE QSMKKISSTI MQVTCQTCKG  420
QFQAVAVPAA ADETSLVVSY MSSANTDGEE S
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-16155209357Zinc finger protein JACKDAW
5b3h_F1e-16155209357Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
15055KKRKRR
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_013607262.1
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_013607262.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A0D3E7H00.0A0A0D3E7H0_BRAOL; Uncharacterized protein
STRINGBo9g070370.10.0(Brassica oleracea)
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]