PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G49770.1
Common NameBHLH95, EN21, F14J22.2, RGE1, ZOU
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 bHLH
Protein Properties Length: 308aa    MW: 34182.5 Da    PI: 6.7116
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G49770.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   8 rErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   Er RR+++++ f++L  llP++     +K +K++i+ +Av  IksL+
                  6*********************6....39*****************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474591.96E-1469131IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088813.33869119IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
CDDcd000834.80E-1374124No hitNo description
PfamPF000101.1E-877120IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.5E-877125IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
Sequence ? help Back to Top
Protein Sequence    Length: 308 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasAT1G49770
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during seed development (PubMed:18567831). Exclusively expressed in the endosperm of developing seeds (PubMed:18849529). {ECO:0000269|PubMed:18567831, ECO:0000269|PubMed:18849529}.
UniprotTISSUE SPECIFICITY: Siliques. Not detected in roots, rosette leaves or flowers. Expressed in endosperm cells. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:18567831}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the basic helix loop helix family of transcription factors. Loss of RGE1 function causes shriveled seeds that contain small embryos. The cuticle in the embryos does not develop normally, possible due to the adeherence of the endosperm to the developing embryo. RGE1 is expressed in the endosperm surrounding region which directly surrounds the developing embryo, however it exerts its effect non autonomously- in the developing embryo. Mutant seedlings are extremely sensitive to dessication due to the abnormal cuticle.
UniProtTranscription factor that controls embryo growth (PubMed:18567831, PubMed:18849529, PubMed:23318634). Regulates endosperm breakdown and embryonic epidermal development. Regulates the expression of SBT2.4/ALE1 (PubMed:18849529, PubMed:23318634). Involved in embryonic cuticle formation upstream of SBT2.4/ALE1 (PubMed:23318634). Does not seem to be a general regulator of endosperm patterning. May control specific signaling pathways that coordinate embryo invasion and breakdown of surrounding endosperm tissues (PubMed:18849529). Required for the production the embryo sheath, an extracuticular endosperm-derived structure at the surface of the embryo. Acts upstream of KRS (PubMed:28696222). {ECO:0000269|PubMed:18567831, ECO:0000269|PubMed:18849529, ECO:0000269|PubMed:23318634, ECO:0000269|PubMed:28696222}.
Function -- GeneRIF ? help Back to Top
  1. RGE1 expression in the endosperm at the heart stage of embryo development plays an important role in controlling embryo growth.
    [PMID: 18567831]
  2. ZOU is not a general regulator of endosperm patterning, but rather controls specific signalling pathways that coordinate embryo invasion and breakdown of surrounding endosperm tissues.
    [PMID: 18849529]
  3. ZHOUPI controls embryonic cuticle formation via a signalling pathway involving the subtilisin protease ABNORMAL LEAF-SHAPE1 and the receptor kinases GASSHO1 and GASSHO2.
    [PMID: 23318634]
  4. ZHOUPI regulates embryonic surface formation via a signaling pathway mediated by ABNORMAL LEAF SHAPE1.
    [PMID: 23531691]
  5. propose that the ZHOUPI/ICE1 complex might have ancient origins, acquiring novel megagametophyte-specific functions in heterosporous land plants that were conserved in the angiosperm endosperm
    [PMID: 24553285]
  6. The recovery of the native ZOU gene expression in the spz2 zou-4 double mutant is caused by transcriptional read-through of the intronic T-DNA as a result of decreased proximal polyadenylation.
    [PMID: 27164978]
  7. RED1 plays important roles in embryo development, seed maturation and plant growth.
    [PMID: 27477025]
  8. ZHOUPI role in the eplant embryo/endosperm separation and the formation of the extracuticular sheath at the seed surface
    [PMID: 28696222]
Cis-element ? help Back to Top
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Small and shriveled seeds. Retarded growth of the embryo after the heart stage, but normal morphogenesis and pattern formation of the embryo and endosperm. {ECO:0000269|PubMed:18567831}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G49770
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4886230.0AF488623.1 Arabidopsis thaliana clone bHLH095 putative bHLH transcription factor mRNA, partial sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_175399.20.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ9FXA30.0BH095_ARATH; Transcription factor bHLH95
STRINGAT1G49770.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP12261548
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
  2. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
  3. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  4. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
  5. Kondou Y, et al.
    RETARDED GROWTH OF EMBRYO1, a new basic helix-loop-helix protein, expresses in endosperm to control embryo growth.
    Plant Physiol., 2008. 147(4): p. 1924-35
  6. Yang S, et al.
    The endosperm-specific ZHOUPI gene of Arabidopsis thaliana regulates endosperm breakdown and embryonic epidermal development.
    Development, 2008. 135(21): p. 3501-9
  7. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
  8. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
  9. Renault H, et al.
    γ-Aminobutyric acid transaminase deficiency impairs central carbon metabolism and leads to cell wall defects during salt stress in Arabidopsis roots.
    Plant Cell Environ., 2013. 36(5): p. 1009-18
  10. Xing Q, et al.
    ZHOUPI controls embryonic cuticle formation via a signalling pathway involving the subtilisin protease ABNORMAL LEAF-SHAPE1 and the receptor kinases GASSHO1 and GASSHO2.
    Development, 2013. 140(4): p. 770-9
  11. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  12. Waters A,Creff A,Goodrich J,Ingram G
    "What we've got here is failure to communicate": zou mutants and endosperm cell death in seed development.
    Plant Signal Behav, 2013. 8(6): p. e24368
  13. Denay G, et al.
    Endosperm breakdown in Arabidopsis requires heterodimers of the basic helix-loop-helix proteins ZHOUPI and INDUCER OF CBP EXPRESSION 1.
    Development, 2014. 141(6): p. 1222-7
  14. Zhang Y, et al.
    Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through.
    Plant Mol. Biol., 2016. 91(4-5): p. 549-61
  15. Fourquin C, et al.
    Mechanical stress mediated by both endosperm softening and embryo growth underlies endosperm elimination in Arabidopsis seeds.
    Development, 2016. 143(18): p. 3300-5
  16. Du Q,Wang H
    Retarded Embryo Development 1 (RED1) regulates embryo development, seed maturation and plant growth in Arabidopsis.
    J Genet Genomics, 2016. 43(7): p. 439-49
  17. Moussu S, et al.
    ZHOUPI and KERBEROS Mediate Embryo/Endosperm Separation by Promoting the Formation of an Extracuticular Sheath at the Embryo Surface.
    Plant Cell, 2017. 29(7): p. 1642-1656