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 Tp57577_TGAC_v2_mRNA30083
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family HD-ZIP
Protein Properties Length: 270aa    MW: 30917.1 Da    PI: 7.7146
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA30083genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.11.5e-18108162256
                                T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
                   Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                                rk+ ++tk+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  Tp57577_TGAC_v2_mRNA30083 108 RKKLRLTKDQSIILEESFKEHNTLNPKQKLALAKQLGLRARQVEVWFQNRRARTK 162
                                788899***********************************************98 PP
2HD-ZIP_I/II125.62.3e-40108197191
                HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekev 84 
                                +kk+rl+k+q+ +LEesF+e+++L+p++K +la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l++en+rL+kev
  Tp57577_TGAC_v2_mRNA30083 108 RKKLRLTKDQSIILEESFKEHNTLNPKQKLALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTDENRRLQKEV 191
                                69********************************************************************************** PP

                HD-ZIP_I/II  85 eeLreel 91 
                                +eLr +l
  Tp57577_TGAC_v2_mRNA30083 192 QELR-AL 197
                                ***9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.2E-192582IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.601.6E-1789165IPR009057Homeodomain-like
SuperFamilySSF466892.35E-1899165IPR009057Homeodomain-like
PROSITE profilePS5007117.184104164IPR001356Homeobox domain
SMARTSM003893.8E-15106168IPR001356Homeobox domain
CDDcd000861.94E-14108165No hitNo description
PfamPF000464.9E-16108162IPR001356Homeobox domain
PRINTSPR000312.2E-5135144IPR000047Helix-turn-helix motif
PROSITE patternPS000270139162IPR017970Homeobox, conserved site
PRINTSPR000312.2E-5144160IPR000047Helix-turn-helix motif
PfamPF021832.1E-11164198IPR003106Leucine zipper, homeobox-associated
SMARTSM003402.9E-27164207IPR003106Leucine 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: 270 aa     Download sequence    Send to blast
MCYIRHEHIF YQKYQGFFNL IDDLILHADR DSETCRGEER SLLLRGIDVN RLPSGADCEE  60
EAGVSSPNST VSSVSGKRSE REVTGEDLDM ERDCSRGISD EEDAETSRKK LRLTKDQSII  120
LEESFKEHNT LNPKQKLALA KQLGLRARQV EVWFQNRRAR TKLKQTEVDC EFLKRCCENL  180
TDENRRLQKE VQELRALKLS PQFYMQMTPP TTLTMCPSCE RVAVPTSAVD ASTRRHPMAP  240
THPRAFPMGP WATAAPIQHR PFDPIRPRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1106112SRKKLRL
2156164RRARTKLKQ
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp57577_TGAC_v2_mRNA30083
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0521290.0BT052129.1 Medicago truncatula clone MTYF9_FA_FB_FC1G-F-12 unknown mRNA.
GenBankBT1352170.0BT135217.1 Medicago truncatula clone JCVI-FLMt-12I21 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003611347.11e-167homeobox-leucine zipper protein HAT4
SwissprotQ054664e-96HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A2K3NVN71e-177A0A2K3NVN7_TRIPR; Homeobox-leucine zipper protein HAT4-like
STRINGAES943051e-167(Medicago truncatula)
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
AT4G16780.16e-85homeobox 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]