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 XP_009133793.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family bHLH
Protein Properties Length: 404aa    MW: 45005.8 Da    PI: 8.9846
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009133793.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH39.78.6e-13226272455
                     HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
             HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                      h+  Er+RR++i +++ eL++llP++      K +K++ L +A++Y++ Lq
  XP_009133793.1 226 VHKLSERKRRNEISKKMCELQDLLPNC-----YKDDKVSLLDEAIKYMRTLQ 272
                     6999**********************8.....6******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.105.2E-16219282IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.44E-16220291IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.11222271IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000832.33E-12225276No hitNo description
PfamPF000102.1E-10226272IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.3E-10228277IPR011598Myc-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: 404 aa     Download sequence    Send to blast
MGKNPYASLS QPNIISPSSS FKPKLSDQAS MELVCENGQI FAKSRRPNNN SYFQNQRTQS  60
ILDLYETEYD EGFKKNIKNL GGSQVVPVSE SQRPQQDEDK KRKINPSKTE SERDVWKRNK  120
RFESSKLMND SLKSLKNVEV TTAPPDEQSI AVGRSAELYF ASSSMLSGGT SRDLSCCSLK  180
KRKYGDMEEE ESTYLSNSDD GSDDGKTRVT TTTRKTVAKK KRSTEVHKLS ERKRRNEISK  240
KMCELQDLLP NCYKDDKVSL LDEAIKYMRT LQLQVQMMSM GNGIIPSTST MLAMGHYSPM  300
GLGMHMGAAA TTTSVPQFLP MNLQGTGFPR INEASSQMLS NFLNHPTGLI PNCPIFSPLE  360
SCSHQFVVPS CFPGTHSTSF TPFSKSAPTS NLEDAMQFKG SNGY
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1219234KKRSTEVHKLSERKRR
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Etiolated seedlings. {ECO:0000269|PubMed:12826627}.
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
PlantRegMapXP_009133793.1
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
GenBankAC2324910.0AC232491.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB049N04, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009133793.10.0PREDICTED: transcription factor PIL1-like
SwissprotQ8L5W80.0PIL1_ARATH; Transcription factor PIL1
TrEMBLM4C8A80.0M4C8A8_BRARP; Uncharacterized protein
STRINGBra000436.1-P0.0(Brassica rapa)
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]