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 Rsa1.0_00336.1_g00001.1
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family bHLH
Protein Properties Length: 257aa    MW: 29015.1 Da    PI: 4.7506
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00336.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
                      HLH  10 rrRRdr.iNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                              +rRRd+ + +++++L++llP++      K + +++L  A+eY+k+Lq
                              5566552789***********9.....699****************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088811.23120169IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.7E-5125175IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000836.64E-8129174No hitNo description
PfamPF000105.0E-5129170IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.22E-11130194IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 257 aa     Download sequence    Send to blast
Functional Description ? help Back to Top
Source Description
UniProtAtypical bHLH transcription factor that regulates photomorphogenesis through modulation of phytochrome (e.g. PHYA) and cryptochrome signalings (Ref.4, PubMed:11090209, PubMed:10995393, PubMed:19482971). Suppresses the transcriptional regulation activity of PIF4 by forming non-DNA-binding heterodimer. {ECO:0000269|PubMed:10995393, ECO:0000269|PubMed:11090209, ECO:0000269|PubMed:19482971, ECO:0000269|Ref.4}.
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Twofold induction by far-red light and 14-fold suppression by red light.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018482591.11e-107PREDICTED: transcription factor HFR1 isoform X1
RefseqXP_018482598.11e-107PREDICTED: transcription factor HFR1 isoform X2
SwissprotQ9FE225e-70HFR1_ARATH; Transcription factor HFR1
TrEMBLA0A3P6CE651e-102A0A3P6CE65_BRACM; Uncharacterized protein
STRINGBra033315.1-P1e-101(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G02340.14e-72bHLH family protein
Publications ? help Back to Top
  1. 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
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
  3. Bou-Torrent J, et al.
    Plant proximity perception dynamically modulates hormone levels and sensitivity in Arabidopsis.
    J. Exp. Bot., 2014. 65(11): p. 2937-47
  4. Luo Q, et al.
    COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis.
    Plant Cell, 2014. 26(6): p. 2441-2456
  5. Adams E,Diaz C,Hong JP,Shin R
    14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs.
    Int J Mol Sci, 2014. 15(12): p. 22801-14
  6. Sheerin DJ, et al.
    Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex.
    Plant Cell, 2015. 27(1): p. 189-201
  7. Karumuri S,Bandopadhyay R
    In silico analysis of the structure and interaction of COP1 protein of Arabidopsis thaliana.
    Indian J. Biochem. Biophys., 2014. 51(5): p. 343-9
  8. Tan CM, et al.
    Arabidopsis HFR1 is a potential nuclear substrate regulated by the Xanthomonas type III effector XopD(Xcc8004).
    PLoS ONE, 2015. 10(2): p. e0117067
  9. Singh SP,Singh SP,Pandey T,Singh RR,Sawant SV
    A novel male sterility-fertility restoration system in plants for hybrid seed production.
    Sci Rep, 2015. 5: p. 11274
  10. Bou-Torrent J, et al.
    Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors.
    Plant Physiol., 2015. 169(3): p. 1584-94
  11. PacĂ­n M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
  12. Hayes S, et al.
    UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis.
    Curr. Biol., 2017. 27(1): p. 120-127
  13. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
  14. Xu X, et al.
    Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis.
    Development, 2017. 144(10): p. 1831-1840
  15. Woloszynska M, et al.
    The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis.
    J. Cell. Sci., 2019.
  16. Yan J, et al.
    Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis.
    Plant Cell, 2017. 29(12): p. 3012-3029
  17. Singh M,Gupta A,Singh D,Khurana JP,Laxmi A
    Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth.
    Sci Rep, 2017. 7(1): p. 16101
  18. Li R, et al.
    Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1.
    Plant Physiol. Biochem., 2018. 123: p. 204-212