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.008G233200.1
Common NameB456_008G233200, LOC105765083
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 HD-ZIP
Protein Properties Length: 302aa    MW: 33836.8 Da    PI: 7.8555
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.008G233200.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.61e-18137191256
                         T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
            Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                         rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  Gorai.008G233200.1 137 RKKLRLSKDQSAILEENFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTK 191
                         788899***********************************************98 PP
2HD-ZIP_I/II128.52.9e-41137226191
         HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                         +kk+rlsk+q+++LEe+F+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+eLr +l
  Gorai.008G233200.1 137 RKKLRLSKDQSAILEENFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQELR-AL 226
                         69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.8E-291111IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.605.4E-18119194IPR009057Homeodomain-like
SuperFamilySSF466891.13E-18126194IPR009057Homeodomain-like
PROSITE profilePS5007117.329133193IPR001356Homeobox domain
SMARTSM003891.1E-15135197IPR001356Homeobox domain
PfamPF000463.4E-16137191IPR001356Homeobox domain
CDDcd000864.20E-15137194No hitNo description
PRINTSPR000312.1E-5164173IPR000047Helix-turn-helix motif
PROSITE patternPS000270168191IPR017970Homeobox, conserved site
PRINTSPR000312.1E-5173189IPR000047Helix-turn-helix motif
PfamPF021832.3E-11193227IPR003106Leucine zipper, homeobox-associated
SMARTSM003401.6E-24193237IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 302 aa     Download sequence    Send to blast
MAEKEDLGLS LSLSFPQNHH SLQRNLRPSL VPSSANSCSS PSTLTLNKHS WNDSSPPSDH  60
NSESFRAEMG SIFRGIDMNI LPSTVDCEEE AGVSSPNSTI SSVSGKRSER EGNGDELEIE  120
KSSSRGISDE EDGDTSRKKL RLSKDQSAIL EENFKEHNTL NPKQKLALAK QLGLRPRQVE  180
VWFQNRRART KLKQTEVDCE FLKRCCENLT EENRRLQKEV QELRALKLSS TQFYMQMTPP  240
TTLTMCTSCE RVAVPPNPPS SATVDPRSHH QLAQTHHRAF HMNPWAPSAA HRPLDALRPR  300
S*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1135141SRKKLRL
2185193RRARTKLKQ
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Predominantly expressed in leaves and stems. {ECO:0000269|PubMed:8106086}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression. {ECO:0000269|PubMed:10477292, ECO:0000269|PubMed:11260495, ECO:0000269|PubMed:8449400}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Rapidly and strongly induced by lowering the ratio of red to far-red light. {ECO:0000269|PubMed:8106086}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012439453.10.0PREDICTED: homeobox-leucine zipper protein HAT4-like
SwissprotQ054661e-105HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A0D2U8C30.0A0A0D2U8C3_GOSRA; Uncharacterized protein
STRINGGorai.008G233200.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15632690
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.13e-99homeobox protein 2
Publications ? help Back to Top
  1. 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]
  2. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
    [PMID:23838958]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  4. Francisco M, et al.
    Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.
    Front Plant Sci, 2016. 7: p. 1010
    [PMID:27462337]
  5. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  6. Ivarson E, et al.
    Effects of Overexpression of WRI1 and Hemoglobin Genes on the Seed Oil Content of Lepidium campestre.
    Front Plant Sci, 2016. 7: p. 2032
    [PMID:28119714]
  7. 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]
  8. Singh M,Gupta A,Singh D,Khurana JP,Laxmi A
    Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth.
    Sci Rep, 2017. 7(1): p. 16101
    [PMID:29170398]