PlantTFDB
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_00760.1_g00003.1
Organism
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: 268aa    MW: 31114.6 Da    PI: 9.2645
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00760.1_g00003.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH231.4e-071351761055
                              HHHHHH.HHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                      HLH  10 rrRRdr.iNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                              +rRRd+ + +++ +L++l+P++      K + +++L k++eY+k+Lq
  Rsa1.0_00760.1_g00003.1 135 KRRRDEmMSNKMRTLQQLVPNC-----HKTDMVSVLDKTIEYMKNLQ 176
                              67777626889**********9.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088812.906126175IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.9E-7131183IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.96E-11131184IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.52E-7135178No hitNo description
PfamPF000101.4E-4135176IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.3E-10135182IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009642Biological Processresponse to light intensity
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0003712Molecular Functiontranscription cofactor activity
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 268 aa     Download sequence    Send to blast
MGLGWRNDVE SLAVEDQDIS VRARSGKDRQ INGLKWSYHY FDRDQADVHV QIVPDISKEE  60
DNLEKNMTSV VPDEHSETGD HHLHIKDYSD SSYNRLYLRN RHAKRKRRRV QIFSDDESED  120
FTRKVPLVTR KSSKKRRRDE MMSNKMRTLQ QLVPNCHKTD MVSVLDKTIE YMKNLQLQFQ  180
VMSIMGMNPY IPQAILNFGM HNHLLTAMGI AHGLNPVKQM TLSPVLPWSW LSPPFINLSF  240
PYSSHQSLLT TPASSQYLCG LVPCPKFL
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1103108KRKRRR
2104108RKRRR
3105109KRRRV
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
SourceLink
PlantRegMapRsa1.0_00760.1_g00003.1
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018487318.10.0PREDICTED: transcription factor HFR1-like isoform X1
SwissprotQ9FE221e-120HFR1_ARATH; Transcription factor HFR1
TrEMBLA0A3P6GUI31e-150A0A3P6GUI3_BRAOL; Uncharacterized protein
STRINGBo8g117510.11e-143(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM140151624
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G02340.11e-109bHLH 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
    [PMID:20219281]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  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
    [PMID:24609653]
  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
    [PMID:24951480]
  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
    [PMID:25501334]
  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
    [PMID:25627066]
  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
    [PMID:25630103]
  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
    [PMID:25647296]
  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
    [PMID:26073981]
  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
    [PMID:26082398]
  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
    [PMID:27105120]
  12. Hayes S, et al.
    UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis.
    Curr. Biol., 2017. 27(1): p. 120-127
    [PMID:27989670]
  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
    [PMID:28316114]
  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
    [PMID:28420710]
  15. Woloszynska M, et al.
    The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis.
    J. Cell. Sci., 2019.
    [PMID:28720596]
  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
    [PMID:29114014]
  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
    [PMID:29170398]
  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
    [PMID:29248678]