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 GSBRNA2T00113560001
Common NameGSBRNA2T00113560001
Organism
Brassica napus
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: 729aa    MW: 83772.6 Da    PI: 9.8507
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00113560001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH48.41.7e-15538583555
                          HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                  HLH   5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                          hne ErrRRdriN+++ +L++llP+a      K +K++iL  ++e++k+Lq
  GSBRNA2T00113560001 538 HNESERRRRDRINQRMRTLQKLLPTA-----SKADKVSILDDVIEHLKQLQ 583
                          *************************9.....7******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF037632.8E-19192291IPR005516Remorin, C-terminal
PROSITE profilePS5088817.06533582IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474597.33E-18536604IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.107.4E-17536598IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000832.89E-7538587No hitNo description
PfamPF000109.4E-13538583IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.9E-16539588IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009704Biological Processde-etiolation
GO:0016021Cellular Componentintegral component of membrane
GO:0016607Cellular Componentnuclear speck
GO:0003690Molecular Functiondouble-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 729 aa     Download sequence    Send to blast
MFLYSGIRIL AIFYNIGRIY EAQTILESLG ENLVKQRRRR VSVSENKQTD MPNLSELAIT  60
DNPALNWLKN QAYWYEKMDY YDEKESEFAT FFFFFFFFCF FFFFFFFFVF SMEEAYKENA  120
KRMREETKRS RKKKTNPVIA KSEVKRINRS FTQDLTIGEE SFKKQQMDNP QKDRREQEIG  180
SSSRTLGLAS APSKADSWEK SQLDKIKLRY EKMKAEIVGW ENERKSAAKL RMEKRKSELQ  240
KRTEINNQHY KTKLARIQVI ADGAKKQLEE KKRSQEAQVQ EKVKKMRRTG KREDSRQGNS  300
NPLPHMCFLH IKTIVIAGTI VSLLYYFNVD QMKIHYMSCR CDCEELENRG GHQDYTTKTK  360
KKKRKAELSN YGVKELTWEN GQLTVHGLGE GVEPTTTSAN LLWTQALNGC ETLESVVHQA  420
ALQPSKLQSQ NGRDHNNSES KDGSCSRKRG YPQEMDCWFS GQEESHRVGH SVTASASGTN  480
MSWASFESGR SLKTARTGDR DYLFSGSETQ ETEGDEQETR GEAGRSNNGR RGRAAAIHNE  540
SERRRRDRIN QRMRTLQKLL PTASKADKVS ILDDVIEHLK QLQAQVQFMS LRANLPQQMM  600
MPQLPPPQSV LSIQHQQQQQ QQQQQQQQQF QMSLLATMAR MGMGGGGNAY GGLVPPHPPL  660
MVPPMDNRDC TNASSASLTD PYSAFLAQTM NMDLYNKMAA AIYRQQSDQT PKVNTGMPSS  720
SSNHEKRD*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1359364KKKKRK
2541546ERRRRD
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Barely detectable in dark-grown seedlings. Induced after 2 hours of light exposure.
UniprotTISSUE SPECIFICITY: Expressed in flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway under prolonged red light. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. May regulate the expression of a subset of genes by binding to the G-box motif. {ECO:0000269|PubMed:15486100, ECO:0000269|PubMed:18252845}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00571DAPTransfer from AT5G61270Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00113560001
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By red light. Stable upon light exposure.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3527340.0AK352734.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-03-L18.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013736938.10.0transcription factor PIF7
SwissprotQ570R70.0PIF7_ARATH; Transcription factor PIF7
TrEMBLA0A3P5ZR110.0A0A3P5ZR11_BRACM; Uncharacterized protein
STRINGBra012972.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM141231822
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G61270.11e-102phytochrome-interacting factor7
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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  4. de Wit M,Ljung K,Fankhauser C
    Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels.
    New Phytol., 2015. 208(1): p. 198-209
    [PMID:25963518]
  5. 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]
  6. 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]
  7. 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]
  8. Peng M, et al.
    Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance.
    Plant Physiol., 2018. 176(2): p. 1341-1351
    [PMID:29187567]
  9. Huang X, et al.
    Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis.
    Elife, 2019.
    [PMID:29926790]