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_05396.1_g00002.1
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: 409aa    MW: 46364.9 Da    PI: 6.4089
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_05396.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH53.73.6e-17259305455
                              HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                      HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                               hn  Er+RRdriN+++  L+el+P++      + +Ka+iL +A++Y+ksLq
  Rsa1.0_05396.1_g00002.1 259 VHNLSERKRRDRINERMKALQELIPHC-----NRTDKASILDEAIDYLKSLQ 305
                              6*************************8.....69*****************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474596.02E-21253316IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.584255304IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000839.16E-17258309No hitNo description
Gene3DG3DSA:4.10.280.107.7E-21259313IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.8E-14259305IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.8E-18261310IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009585Biological Processred, far-red light phototransduction
GO:0009693Biological Processethylene biosynthetic process
GO:0010244Biological Processresponse to low fluence blue light stimulus by blue low-fluence system
GO:0010600Biological Processregulation of auxin biosynthetic process
GO:0010928Biological Processregulation of auxin mediated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 409 aa     Download sequence    Send to blast
MEQLFPGWNL EDNFHVSTSK RSIRPEDELV ELFWRDGQVV LQSQVRREPS VQVQNHKHDQ  60
ALREPNNTFL VNQETVQKHN NTLQEDQETV SWIQYPSEDV IDPFESEFSS HFFSSIDHLD  120
GPDHPEKPQT IEDAIKHEAQ TMAPPKFRSS VVTIGPSHCG SSQSTNDHQV THPQVPMSDR  180
SKNAKERLDT SSGGLSGCSK ENESGRNVTI SRKRKHVMDT DQESVSQSDV SLMSTDDQVM  240
GNKSSQRSGS TRRSRAAEVH NLSERKRRDR INERMKALQE LIPHCNRTDK ASILDEAIDY  300
LKSLQMQLQV MWMGRGMAAA AAIPMMFPGV QSSQYINQMA MQSQMLQPQF PVMNRSVAQN  360
HPGLVCQNPV MQLQMQAQNH ILSEQLARYM GGFPPMPATT QVSEYVTVV
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1263268ERKRRD
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway to promote the shade-avoidance response. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. Promotes ethylene activity in the dark. May regulate the expression of a subset of genes by binding to the G-box motif. Might be involved in the integration of light-signals to control both circadian and photomorphogenic processes. Activated by CRY1 and CRY2 in response to low blue light (LBL) by direct binding at chromatin on E-box variant 5'-CA[CT]GTG-3' to stimulate specific gene expression to adapt global physiology (e.g. hypocotyl elongation in low blue light) (PubMed:26724867). {ECO:0000269|PubMed:12826627, ECO:0000269|PubMed:15356333, ECO:0000269|PubMed:15486100, ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474, ECO:0000269|PubMed:18065691, ECO:0000269|PubMed:26724867}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00082ChIP-seqTransfer from AT3G59060Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_05396.1_g00002.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Follow a free-running robust circadian rhythm, with higher levels during the light phase. Rapidly induced by light in etiolated plants. Up-regulated by white light. Rapid degradation after red light exposure (at protein level). Accumulates to high levels in the dark, is selectively degraded in response to red light and remains at high levels under shade-mimicking conditions. {ECO:0000269|PubMed:12826627, ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018478702.10.0PREDICTED: transcription factor PIF5-like isoform X1
SwissprotQ84LH80.0PIF5_ARATH; Transcription factor PIF5
TrEMBLA0A3P5YNP80.0A0A3P5YNP8_BRACM; Uncharacterized protein
STRINGXP_006402726.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM34682561
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G59060.10.0phytochrome interacting factor 3-like 6
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. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
    [PMID:23838958]
  3. Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ
    Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation.
    Plant Cell, 2013. 25(8): p. 2892-906
    [PMID:23933882]
  4. Mannen K, et al.
    Coordinated transcriptional regulation of isopentenyl diphosphate biosynthetic pathway enzymes in plastids by phytochrome-interacting factor 5.
    Biochem. Biophys. Res. Commun., 2014. 443(2): p. 768-74
    [PMID:24342623]
  5. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  6. Di C, et al.
    Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.
    Plant J., 2014. 80(5): p. 848-61
    [PMID:25256571]
  7. Dornbusch T,Michaud O,Xenarios I,Fankhauser C
    Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation.
    Plant Cell, 2014. 26(10): p. 3911-21
    [PMID:25281688]
  8. Seaton DD, et al.
    Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature.
    Mol. Syst. Biol., 2015. 11(1): p. 776
    [PMID:25600997]
  9. Filo J, et al.
    Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5.
    Plant Signal Behav, 2015. 10(3): p. e992707
    [PMID:25738547]
  10. Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T
    Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94
    [PMID:26193333]
  11. Galvão VC,Collani S,Horrer D,Schmid M
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana.
    Plant J., 2015. 84(5): p. 949-62
    [PMID:26466761]
  12. Miyazaki Y, et al.
    Enhancement of hypocotyl elongation by LOV KELCH PROTEIN2 production is mediated by auxin and phytochrome-interacting factors in Arabidopsis thaliana.
    Plant Cell Rep., 2016. 35(2): p. 455-67
    [PMID:26601822]
  13. Yue J, et al.
    TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.
    Plant Physiol., 2016. 170(3): p. 1381-97
    [PMID:26704640]
  14. Pacín 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]
  15. Fernández V,Takahashi Y,Le Gourrierec J,Coupland G
    Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days.
    Plant J., 2016. 86(5): p. 426-40
    [PMID:27117775]
  16. Martin G,Soy J,Monte E
    Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.
    Front Plant Sci, 2016. 7: p. 962
    [PMID:27458465]
  17. Gray JA,Shalit-Kaneh A,Chu DN,Hsu PY,Harmer SL
    The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size.
    Plant Physiol., 2017. 173(4): p. 2308-2322
    [PMID:28254761]
  18. 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]
  19. Wei Z, et al.
    Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5.
    Plant Physiol., 2017. 174(2): p. 1260-1273
    [PMID:28438793]
  20. Shor E,Paik I,Kangisser S,Green R,Huq E
    PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis.
    New Phytol., 2017. 215(1): p. 217-228
    [PMID:28440582]
  21. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
    [PMID:28711729]
  22. Swain S,Jiang HW,Hsieh HL
    FAR-RED INSENSITIVE 219/JAR1 Contributes to Shade Avoidance Responses of Arabidopsis Seedlings by Modulating Key Shade Signaling Components.
    Front Plant Sci, 2017. 8: p. 1901
    [PMID:29163619]