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 Gorai.006G008800.1
Common NameB456_006G008800
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family bHLH
Protein Properties Length: 354aa    MW: 39959.6 Da    PI: 6.0074
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.006G008800.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH53.44.5e-17188234455
                         HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                 HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                          hn  ErrRRdriN+++  L+el+P++      K +Ka++L +A+eY+ksLq
  Gorai.006G008800.1 188 VHNLSERRRRDRINEKMRALQELIPHC-----NKTDKASMLDEAIEYLKSLQ 234
                         6*************************8.....6******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474593.53E-21183250IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.457184233IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000833.79E-18187238No hitNo description
PfamPF000102.2E-14188234IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.104.5E-21188244IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.3E-18190239IPR011598Myc-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: 354 aa     Download sequence    Send to blast
MSFKASICLA MNHCSSDWNF ESDLPISNQK KLLDNELVEL LWQNGKVVLQ SQTHKKQDDE  60
TVSWIQHPFE ESFEKEMFSN FFSEFPVYDP MDHQHEQQED DKNLSRGSSN GIGTTSTGLS  120
VGTSKDDEDD DNGGQVENEK GTSGGVTSSQ KRKNRDGRED YECQCEFAEV KPVRRSGSCR  180
RQSRAAEVHN LSERRRRDRI NEKMRALQEL IPHCNKTDKA SMLDEAIEYL KSLQLQLQVM  240
WMGNGMAPMM FPGIQHYMSP MAMGTAPPTM PSIQNQRFIQ NPTFSEQYAR FLGFHHMQTA  300
SQPINMFGYG SQTTPQSPTV LGFSNGSNPL NGGTTATNNT SLSGKIVLWR LLY*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1192197ERRRRD
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the node portions of the stem. Expressed in the leaves and the basal part of shoots. {ECO:0000269|PubMed:22984180}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that may act as negative regulator of phyB-dependent light signal transduction (PubMed:17485859). Transcription activator that acts as positive regulator of internode elongation. May function via regulation of cell wall-related genes. May play a role in a drought-associated growth-restriction mechanism in response to drought stress (PubMed:22984180). {ECO:0000269|PubMed:17485859, ECO:0000269|PubMed:22984180}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00082ChIP-seqTransfer from AT3G59060Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by light in dark-grown etiolated seedlings (PubMed:17485859). Circadian oscillation under 12 h light/12 h dark cycle conditions, with peaks in the middle of the light period (PubMed:17485859, PubMed:22984180). Down-regulated by cold and drought stresses (PubMed:22984180). {ECO:0000269|PubMed:17485859, ECO:0000269|PubMed:22984180}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHQ5258024e-67HQ525802.1 Gossypium herbaceum clone NBRI_D_EYT27PB02DXEGO simple sequence repeat marker, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016727800.10.0PREDICTED: transcription factor PIF4-like
RefseqXP_016727801.10.0PREDICTED: transcription factor PIF4-like
SwissprotQ10CH52e-55PIL13_ORYSJ; Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13
TrEMBLA0A0D2SQ620.0A0A0D2SQ62_GOSRA; Uncharacterized protein
STRINGGorai.006G008800.10.0(Gossypium raimondii)
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
AT3G59060.41e-39phytochrome interacting factor 3-like 6
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Nakamura Y,Kato T,Yamashino T,Murakami M,Mizuno T
    Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.
    Biosci. Biotechnol. Biochem., 2007. 71(5): p. 1183-91
    [PMID:17485859]
  3. Zhao XL,Shi ZY,Peng LT,Shen GZ,Zhang JL
    An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15.
    N Biotechnol, 2011. 28(6): p. 788-97
    [PMID:21549224]
  4. Todaka D, et al.
    Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(39): p. 15947-52
    [PMID:22984180]
  5. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]