PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 904169
Common NameARALYDRAFT_904169
Organism
Arabidopsis lyrata
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: 414aa    MW: 46567.4 Da    PI: 9.4308
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
904169genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH383.1e-12230276455
             HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
     HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
              h+  Er+RRd+ N+++  L+++lP++      K +Ka+ L +Av+Y++ Lq
  904169 230 VHKLYERKRRDEFNKKMRALQDILPNC-----YKDDKASLLDEAVKYMRTLQ 276
             59999*********************8.....6******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.101.0E-16223286IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.7E-17224300IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000834.15E-11224280No hitNo description
PROSITE profilePS5088814.958226275IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000107.5E-10230276IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.3E-11232281IPR011598Myc-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: 414 aa     Download sequence    Send to blast
MEEKPLASSS SQPNMISPSS SFKPKLKDQD YMELVCENGQ ILAKGRRHKN NGSFQNQRRQ  60
SLLDLYETEY NEGFKKNIKN LGDTQVVPVN ESQPQQDKEN NEHMNKKKLK SSKIESERNV  120
SKSNKRVESS TLIDDSKGPK NVEVTRTPPD EQSAAVGRST ELYSASSSMF SRGSSRDLSL  180
CSLKRKHGDI EEEESTYLSN NPDDESDDAK TQVHARIRKP VTKRKRSTEV HKLYERKRRD  240
EFNKKMRALQ DILPNCYKDD KASLLDEAVK YMRTLQHQVQ MMSMGNGLIR PPMMLPMGHY  300
PPMGLGMHVG AAATPTSVPQ FLPMNIQGTS FPGINNASSQ MLRFLNHPTG LIPNTPIFSP  360
LENCSQQFVV PSCVPQTHAT SFTQFPKSAS TSNLEDAMQY RGSNGYSYYP SQN*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1223238RKRSTEVHKLYERKRR
2234239ERKRRD
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
PlantRegMap904169
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
RefseqXP_002882098.10.0transcription factor PIL1
SwissprotQ8L5W80.0PIL1_ARATH; Transcription factor PIL1
TrEMBLD7LFX40.0D7LFX4_ARALL; Uncharacterized protein
STRINGscaffold_403670.10.0(Arabidopsis lyrata)
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]