PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G66350.1
Common NameSHI
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family SRS
Protein Properties Length: 331aa    MW: 35376.8 Da    PI: 8.2647
Description Lateral root primordium (LRP) protein-related
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G66350.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF702227.42.7e-701152633154
       DUF702   3 sgtasCqdCGnqakkdCaheRCRtCCksrgfdCathvkstWvpaakrrerqqqlaaasskaaasaaeaaskrkrelkskkqsalsstklssaeskkel 100
                  sg+ sCqdCGnq+kkdC+h+RCRtCCksrg+dC thvkstWvpaakrrerqqql++ ++   ++   + +kr+re   +++++++ t+++s++++  l
  AT5G66350.1 115 SGGPSCQDCGNQSKKDCSHMRCRTCCKSRGLDCPTHVKSTWVPAAKRRERQQQLSTGQQ--PQQLGGSVPKRQRERIPARSTSMAYTRIPSNNTS-GL 209
                  68889***********************************************9998755..55779999*********************99866.99 PP

       DUF702 101 etsslPeevsseavfrcvrvssvddgeeelaYqtavsigGhvfkGiLydqGlee 154
                  e+ ++P+evss+avfrcvrvssvdd+eee+aY+tavsigGhvfkG+LydqG++e
  AT5G66350.1 210 EVGNFPPEVSSSAVFRCVRVSSVDDEEEEYAYKTAVSIGGHVFKGVLYDQGPAE 263
                  999************************************************986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF051422.1E-64117262IPR007818Protein of unknown function DUF702
TIGRFAMsTIGR016231.9E-26119161IPR006510Zinc finger, lateral root primordium type 1
TIGRFAMsTIGR016246.9E-26214261IPR006511Lateral Root Primordium type 1, C-terminal
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007275Biological Processmulticellular organism development
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009851Biological Processauxin biosynthetic process
GO:0009938Biological Processnegative regulation of gibberellic acid mediated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0046982Molecular Functionprotein heterodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000016anatomylateral root primordium
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0004709anatomyaxillary bud
PO:0005660anatomyhydathode
PO:0006332anatomyseed funicle
PO:0009009anatomyplant embryo
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0009073anatomystigma
PO:0009074anatomystyle
PO:0004507developmental stageplant embryo bilateral stage
PO:0007057developmental stageseed germination stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 331 aa     Download sequence    Send to blast
MAGFFSLGHG GGGNTPDNHR TNTNNPSSSG TESWLWCRNP NSNADGGEAG PSYKGTLELW  60
QHPNNQEIIF QQQQQQQQRL DLYTSAAGLG VGPSNRSLIE TSGGALMMMR SGSGSGGPSC  120
QDCGNQSKKD CSHMRCRTCC KSRGLDCPTH VKSTWVPAAK RRERQQQLST GQQPQQLGGS  180
VPKRQRERIP ARSTSMAYTR IPSNNTSGLE VGNFPPEVSS SAVFRCVRVS SVDDEEEEYA  240
YKTAVSIGGH VFKGVLYDQG PAERSSSGGG SQPLNLITAG PSASSSSPNV SCNNGVVGST  300
SDHYIDPASL NYPTPINTFM TGTHFFSNSR S
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO49298020.0
Genevisible247093_at0.0
Expression AtlasAT5G66350-
AtGenExpressAT5G66350-
ATTED-IIAT5G66350-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In germinating seeds, first detected at about 48 h after imbibition. In young seedlings grown in continuous light, present in the root/shoot transition zone, in the apex, and in the apical region of the cotyledons. Later observed in lateral root primordia and in emerging lateral roots, particularly in the root tips, as well as in the shoot apex and in the new leaves, especially in the apical and lateral hydathodes. In adult plants, accumulates in lateral root tips, lateral root primordia, and axillary shoot primordia. In flowers, expressed in the style and stigmatic surface of the pistil and in the receptacle (base) of the flower throughout the development of the pistil until anthesis and later in the silique. Fades out after fertilization. {ECO:0000269|PubMed:11706176, ECO:0000269|PubMed:16740146}.
UniprotTISSUE SPECIFICITY: Expressed in young organs such as shoot apices and root tips. Present in roots, stems, flowers, leaves, hydathodes and siliques. {ECO:0000269|PubMed:10368174, ECO:0000269|PubMed:11706176}.
Functional Description ? help Back to Top
Source Description
TAIRA member of SHI gene family. Arabidopsis thaliana has ten members that encode proteins with a RING finger-like zinc finger motif. Despite being highly divergent in sequence, many of the SHI-related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis. Shi mutant is dominant, has dwarf phenotype. Loss of function mutations have no observable phenotype. Putative zinc finger protein. Involved in the response to gibberellic acid.
UniProtTranscription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering. Synergistically with other SHI-related proteins, regulates gynoecium, stamen and leaf development in a dose-dependent manner, controlling apical-basal patterning. Promotes style and stigma formation, and influences vascular development during gynoecium development. May also have a role in the formation and/or maintenance of the shoot apical meristem (SAM). Suppressor of the gibberellin (GA) signal transduction. {ECO:0000269|PubMed:10368174, ECO:0000269|PubMed:11706176, ECO:0000269|PubMed:16740146}.
Function -- GeneRIF ? help Back to Top
  1. At least six SHI-related genes contribute to carpel fusion as well as to the formation of all marginal tissues in the apical part of the gynoecium.
    [PMID: 16740146]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G66350.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDgibberellin
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: High gibberellin (GA) levels associated with dwarfism, short hypocotyl, narrow leaves, reduced apical dominance, and late flowering, but more flowers. {ECO:0000269|PubMed:10368174, ECO:0000269|PubMed:11706176, ECO:0000269|PubMed:16740146}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G66350
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1525550.0AF152555.1 Arabidopsis thaliana putative zinc finger protein SHI (SHI) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_201436.10.0protein SHORT INTERNODES
SwissprotQ9XGX00.0SHI_ARATH; Protein SHORT INTERNODES
TrEMBLR0EWR70.0R0EWR7_9BRAS; Uncharacterized protein
STRINGAT5G66350.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM34192864
Representative plantOGRP18721140
Publications ? help Back to Top
  1. Fridborg I,Kuusk S,Moritz T,Sundberg E
    The Arabidopsis dwarf mutant shi exhibits reduced gibberellin responses conferred by overexpression of a new putative zinc finger protein.
    Plant Cell, 1999. 11(6): p. 1019-32
    [PMID:10368174]
  2. Fridborg I,Kuusk S,Robertson M,Sundberg E
    The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley.
    Plant Physiol., 2001. 127(3): p. 937-48
    [PMID:11706176]
  3. Smith HM,Hake S
    The interaction of two homeobox genes, BREVIPEDICELLUS and PENNYWISE, regulates internode patterning in the Arabidopsis inflorescence.
    Plant Cell, 2003. 15(8): p. 1717-27
    [PMID:12897247]
  4. Kuusk S,Sohlberg JJ,Magnus Eklund D,Sundberg E
    Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner.
    Plant J., 2006. 47(1): p. 99-111
    [PMID:16740146]
  5. L
    Production of compact plants by overexpression of AtSHI in the ornamental Kalancho
    Plant Biotechnol. J., 2010. 8(2): p. 211-22
    [PMID:20051037]
  6. Eklund DM, et al.
    Homologues of the Arabidopsis thaliana SHI/STY/LRP1 genes control auxin biosynthesis and affect growth and development in the moss Physcomitrella patens.
    Development, 2010. 137(8): p. 1275-84
    [PMID:20223761]
  7. Zawaski C, et al.
    SHORT INTERNODES-like genes regulate shoot growth and xylem proliferation in Populus.
    New Phytol., 2011. 191(3): p. 678-91
    [PMID:21564099]
  8. Eklund DM, et al.
    Expression of Arabidopsis SHORT INTERNODES/STYLISH family genes in auxin biosynthesis zones of aerial organs is dependent on a GCC box-like regulatory element.
    Plant Physiol., 2011. 157(4): p. 2069-80
    [PMID:21976484]
  9. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
    [PMID:22995285]
  10. Baylis T,Cierlik I,Sundberg E,Mattsson J
    SHORT INTERNODES/STYLISH genes, regulators of auxin biosynthesis, are involved in leaf vein development in Arabidopsis thaliana.
    New Phytol., 2013. 197(3): p. 737-50
    [PMID:23293954]