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 AT2G01940.1
Common NameATIDD15, F14H20.1, IDD15, SGR5
Organism
Arabidopsis thaliana
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 C2H2
Protein Properties Length: 445aa    MW: 50140.4 Da    PI: 9.3197
Description C2H2-like zinc finger protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G01940.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.51.1e-057395123
                 EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                 y C++C++ F r  nL+ H r+H
  AT2G01940.1 73 YICEICNQGFQRDQNLQMHRRRH 95
                 89********************9 PP
2zf-C2H214.50.0001151173123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  ++C+ C+k +  +s++k H++t+
  AT2G01940.1 151 WVCERCSKGYAVQSDYKAHLKTC 173
                  58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.97E-57096No hitNo description
Gene3DG3DSA:3.30.160.601.3E-57295IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00657395IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8667395IPR007087Zinc finger, C2H2
PROSITE patternPS0002807595IPR007087Zinc finger, C2H2
SMARTSM00355160115145IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.8E-4142172IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM00355100151178IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0005058anatomyshoot axis endodermis
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 445 aa     Download sequence    Send to blast
MRTDQVMLSN KNTNTCCVVS SSSSDPFLSS SENGVTTTNT STQKRKRRPA GTPDPDAEVV  60
SLSPRTLLES DRYICEICNQ GFQRDQNLQM HRRRHKVPWK LLKRDNNIEV KKRVYVCPEP  120
TCLHHNPCHA LGDLVGIKKH FRRKHSNHKQ WVCERCSKGY AVQSDYKAHL KTCGTRGHSC  180
DCGRVFSRVE SFIEHQDNCS ARRVHREPPR PPQTAVTVPA CSSRTASTVS TPSSETNYGG  240
TVAVTTPQPL EGRPIHQRIS SSILTNSSNN LNLELQLLPL SSNQNPNQEN QQQKVKEPSH  300
HHNHNHDTTN LNLSIAPSSS YQHYNNFDRI KEIMASEQIM KIAMKEKAYA EEAKREAKRQ  360
REIAENEFAN AKKIRQKAQA ELERAKFLKE QSMKKISSTI MQVTCQTCKG QFQAVAVPAA  420
TADETSLVVS YMSSANTDGE LENGF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-18149201557Zinc finger protein JACKDAW
5b3h_F4e-18149201557Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.420190.0flower| inflorescence| seed| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible265249_at0.0
Expression AtlasAT2G01940-
AtGenExpressAT2G01940-
ATTED-IIAT2G01940-
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
TAIRMay be involved in an early event in shoot gravitropism such as gravity perception and/or a signaling process subsequent to amyloplast sedimentation as a putative transcription factor in gravity-perceptive cells.
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}.
Function -- GeneRIF ? help Back to Top
  1. SGR5 may be involved in an early event in shoot gravitropism such as gravity perception and/or a signaling process subsequent to amyloplast sedimentation as a putative transcription factor in gravity-perceptive cells. [SGR5]
    [PMID: 16813575]
  2. Loss of SGR5 regulatory activity affects starch accumulation in Arabidopsis shoot tissues and causes decreased sensitivity to gravity and diminished circumnutational movements.
    [PMID: 18259878]
  3. The thermoresponsive alternative splicing of SGR5 is proposed to provide an adaptation strategy by which plants protect the shoots from hot air under high temperature stress in natural habitats.
    [PMID: 26256266]
  4. the identification of INDETERMINATE DOMAIN15 (IDD15) and INDOLE-3-ACETIC ACID 17 (IAA17) in Arabidopsis that interacted with ZAT6 in vivo provided new insight of ZAT6-mediated auxin signaling. Further investigation showed that ZAT6 repressed the transcription activation of IDD15 on the YUC2 promoter
    [PMID: 29607541]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00254DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G01940.1
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
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: In sgr5-2 and sgr5-3, abnormal inflorescence stems gravitropism but normal hypocotyl and root gravitropism. Slow amyloplasts sedimentation associated with lower amyloplast starch levels. Attenuated stem circumnutation movement. No visible phenotype (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G01940
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2267030.0AK226703.1 Arabidopsis thaliana mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL07-61-I21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_178303.20.0C2H2-like zinc finger protein
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A178VUU80.0A0A178VUU8_ARATH; SGR5
STRINGBostr.0556s0022.1.p0.0(Boechera stricta)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  3. Castelli V, et al.
    Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.
    Genome Res., 2004. 14(3): p. 406-13
    [PMID:14993207]
  4. Englbrecht CC,Schoof H,B
    Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
    BMC Genomics, 2004. 5(1): p. 39
    [PMID:15236668]
  5. Colasanti J, et al.
    The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.
    BMC Genomics, 2006. 7: p. 158
    [PMID:16784536]
  6. Morita MT, et al.
    A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems.
    Plant J., 2006. 47(4): p. 619-28
    [PMID:16813575]
  7. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
    [PMID:16920880]
  8. Tanimoto M,Tremblay R,Colasanti J
    Altered gravitropic response, amyloplast sedimentation and circumnutation in the Arabidopsis shoot gravitropism 5 mutant are associated with reduced starch levels.
    Plant Mol. Biol., 2008. 67(1-2): p. 57-69
    [PMID:18259878]
  9. Panjabi P, et al.
    Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes.
    BMC Genomics, 2008. 9: p. 113
    [PMID:18315867]
  10. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  11. Cui D, et al.
    The arabidopsis IDD14, IDD15, and IDD16 cooperatively regulate lateral organ morphogenesis and gravitropism by promoting auxin biosynthesis and transport.
    PLoS Genet., 2013. 9(9): p. e1003759
    [PMID:24039602]
  12. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  13. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. Yamauchi Y,Fukaki H,Fujisawa H,Tasaka M
    Mutations in the SGR4, SGR5 and SGR6 loci of Arabidopsis thaliana alter the shoot gravitropism.
    Plant Cell Physiol., 1997. 38(5): p. 530-5
    [PMID:9210330]