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 maker-scaffold06976-snap-gene-0.12-mRNA-1
Organism
Castanea mollissima
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Castanea
Family HD-ZIP
Protein Properties Length: 251aa    MW: 28489.2 Da    PI: 7.684
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
maker-scaffold06976-snap-gene-0.12-mRNA-1genomeTHGPView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.36.2e-1987141256
                                                T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                                   Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                                                rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  maker-scaffold06976-snap-gene-0.12-mRNA-1  87 RKKLRLSKDQSAVLEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTK 141
                                                788899***********************************************98 PP
2HD-ZIP_I/II130.28.1e-4287176191
                                HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkr 68 
                                                +kk+rlsk+q+++LEesF+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr
  maker-scaffold06976-snap-gene-0.12-mRNA-1  87 RKKLRLSKDQSAVLEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKR 154
                                                69****************************************************************** PP

                                HD-ZIP_I/II  69 aydalkeenerLekeveeLreel 91 
                                                ++++l++en+rL+kev+eLr +l
  maker-scaffold06976-snap-gene-0.12-mRNA-1 155 CCENLTDENRRLQKEVQELR-AL 176
                                                *******************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.8E-21961IPR006712HD-ZIP protein, N-terminal
SuperFamilySSF466891.09E-1878144IPR009057Homeodomain-like
PROSITE profilePS5007117.47583143IPR001356Homeobox domain
SMARTSM003899.5E-1785147IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.9E-1887141IPR009057Homeodomain-like
CDDcd000861.13E-1587144No hitNo description
PfamPF000462.1E-1687141IPR001356Homeobox domain
PRINTSPR000311.5E-5114123IPR000047Helix-turn-helix motif
PROSITE patternPS000270118141IPR017970Homeobox, conserved site
PRINTSPR000311.5E-5123139IPR000047Helix-turn-helix motif
SMARTSM003402.9E-27143186IPR003106Leucine zipper, homeobox-associated
PfamPF021831.9E-11143177IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008283Biological Processcell proliferation
GO:0009641Biological Processshade avoidance
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0009826Biological Processunidimensional cell growth
GO:0010016Biological Processshoot system morphogenesis
GO:0010017Biological Processred or far-red light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048364Biological Processroot development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 251 aa     Download sequence    Send to blast
MMVEKEDLDR NSETCRGDTR SFLRGIDVNR LPSTADCEEE AGVSSPNSTL SSVSGKRSER  60
EALCEELDIE RACSRGISDE EDGETSRKKL RLSKDQSAVL EESFKEHNTL NPKQKLALAK  120
QLGLRPRQVE VWFQNRRART KLKQTEVDCE FLKRCCENLT DENRRLQKEV QELRALKLSP  180
QFYMQMTPPT TLTMCPSCER VGVPPSSSST VDARSHQMGP THQRPIPINP WAPTPSSIPH  240
RPFDAVLHPR S
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
18591SRKKLRL
2135143RRARTKLKQ
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_023921420.11e-175homeobox-leucine zipper protein HAT4
SwissprotQ054661e-101HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A2N9F0H61e-156A0A2N9F0H6_FAGSY; Uncharacterized protein
STRINGVIT_00s0299g00100.t011e-150(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF123934105
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.12e-95homeobox protein 2
Publications ? help Back to Top
  1. 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]
  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. 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]
  4. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  5. 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]
  6. 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]
  7. 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]