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 Bostr.25993s0069.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family bHLH
Protein Properties Length: 411aa    MW: 45981.5 Da    PI: 8.4451
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.25993s0069.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH40.26.3e-13228274455
                           HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                   HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                            h+  Er+RRd+ N+++  L++llP++      K +Ka+ L +A++Y++ Lq
  Bostr.25993s0069.1.p 228 VHKLSERKRRDEFNKKMRALQDLLPNC-----DKDDKASLLDEAIKYMRTLQ 274
                           6999**********************9.....8******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.102.9E-17221286IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474598.64E-18222292IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.81E-12222278No hitNo description
PROSITE profilePS5088815.84224273IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.6E-10228274IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003538.1E-12230279IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009641Biological Processshade avoidance
GO:0010017Biological Processred or far-red light signaling pathway
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 411 aa     Download sequence    Send to blast
MEGKPLASSS SQPSSSFKQK LNDQDYMELV CENGQILAKS RRPKNNGSFQ NQRKQSLLDL  60
YETEYYDGIK KDIKNLGDTQ VVPVSESQPQ QDKENDEQMN NNKKKIKSSK IEFERNVSKS  120
HKRVESSTLI DDSAKGPKNV EVTTAPPDQQ SAAVGRSTEL YFASSSMFSQ GTSRDQSFCS  180
LKRKHGDIEE EESTYLSNNS DDESDDEKTQ VHVRTRKPVT KRKRSTEVHK LSERKRRDEF  240
NKKMRALQDL LPNCDKDDKA SLLDEAIKYM RTLQLQVQMM SMGNGLIRQP TMLPMGHYSP  300
MCLGMHMGAA AATISVPQFL PTNVQGTGYP GIINASSQML SFLNHSTGLI PNSPIFSPLE  360
NCSQQFVVPS CVPQKTQATS FTQFPKSAST SNLEDAMQFR GSNGYYCSQN *
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1221236RKRSTEVHKLSERKRR
2232237ERKRRD
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. {ECO:0000269|PubMed:14668869, ECO:0000269|PubMed:16565297, ECO:0000269|PubMed:16891401}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapBostr.25993s0069.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. {ECO:0000269|PubMed:14668869, ECO:0000269|PubMed:16565297, ECO:0000269|PubMed:16891401}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY9548400.0AY954840.1 Arabidopsis thaliana hypothetical protein (At2g46970) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_182220.20.0phytochrome interacting factor 3-like 1
SwissprotQ8L5W80.0PIL1_ARATH; Transcription factor PIL1
TrEMBLA0A178VNL30.0A0A178VNL3_ARATH; PIL1
STRINGBostr.25993s0069.1.p0.0(Boechera stricta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM139371725
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G46970.10.0phytochrome interacting factor 3-like 1
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. 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]
  3. 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]