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 Araha.12285s0010.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family HD-ZIP
Protein Properties Length: 651aa    MW: 72543.6 Da    PI: 7.95
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.12285s0010.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox52.96.3e-174798556
                          SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
              Homeobox  5 ttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                          +++t++q++eLe+++ +n+ p++++r eL ++l+++ +qVk+WFqN+R + k
  Araha.12285s0010.1.p 47 HRHTAYQTQELENFYLENPLPTEDQRYELGQRLNMEPKQVKFWFQNKRNQVK 98
                          579*********************************************8765 PP
2START156.52.2e-4926143734206
                           EEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEE CS
                 START  34 lqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetla....kaetlevissg......galqlmvaelqalsplvp.Rdfvf 111
                           ++k+ ++    +ea+r++g+v+m++ +lv++++d+  +W   +a     a+t +vi +g      g lq+++ae+q++splvp R ++f
  Araha.12285s0010.1.p 261 VTKP-PG--HVVEASREIGLVPMTCLTLVKTFMDTE-KWVDVFAsivpVASTRKVIPTGsggtksGSLQQIQAEFQVISPLVPkRQVTF 345
                           3333.22..67*************************.*******9999***************************************** PP

                           EEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHT CS
                 START 112 vRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslvksglaegaktwvatl 200
                           +Ry+++l+ g wv+vd  v+++q+p+   s+  +++lpSg+ i +++ng+s+vtw+e+++++++++h l+++l++sg+  ga +w+atl
  Araha.12285s0010.1.p 346 LRYCKELRHGLWVVVD--VTPDQNPT-LLSYGGSNRLPSGLFIADMANGYSQVTWIEQAEYNESHIHPLYQPLIGSGIGLGATRWLATL 431
                           ****************..********.7************************************************************* PP

                           XXXXXX CS
                 START 201 qrqcek 206
                           qr+ce+
  Araha.12285s0010.1.p 432 QRHCES 437
                           ****95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.61E-173298IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.601.4E-1836100IPR009057Homeodomain-like
PROSITE profilePS5007115.40240100IPR001356Homeobox domain
SMARTSM003894.5E-1541104IPR001356Homeobox domain
CDDcd000868.90E-154498No hitNo description
PfamPF000463.6E-144797IPR001356Homeobox domain
PROSITE profilePS5084835.826208440IPR002913START domain
SuperFamilySSF559611.01E-21209438No hitNo description
CDDcd088751.46E-92212436No hitNo description
SMARTSM002347.2E-48217437IPR002913START domain
PfamPF018521.7E-45261437IPR002913START domain
SuperFamilySSF559615.59E-8452631No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006349Biological Processregulation of gene expression by genetic imprinting
GO:0009911Biological Processpositive regulation of flower development
GO:0031047Biological Processgene silencing by RNA
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008289Molecular Functionlipid binding
GO:0042803Molecular Functionprotein homodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 651 aa     Download sequence    Send to blast
MNEQGDDFDA VGNIPNPSGA ENGESDHMID ATSGDNDQDG GRMRRTHRHT AYQTQELENF  60
YLENPLPTED QRYELGQRLN MEPKQVKFWF QNKRNQVKIN SDRLENITLR EDHDRLLLTQ  120
HQLRSAMLHC SCNICGRATN CRDIDYEVQK LIVENTILER EINQLYSKIP SRPNQMLVSP  180
SQPPHCSSSN PGINATPELG LGGGTRTTEK ERSMFLDLAI KALKELLELG EMDCPFGKID  240
SRSSKAVSLI NEKYKNASNN VTKPPGHVVE ASREIGLVPM TCLTLVKTFM DTEKWVDVFA  300
SIVPVASTRK VIPTGSGGTK SGSLQQIQAE FQVISPLVPK RQVTFLRYCK ELRHGLWVVV  360
DVTPDQNPTL LSYGGSNRLP SGLFIADMAN GYSQVTWIEQ AEYNESHIHP LYQPLIGSGI  420
GLGATRWLAT LQRHCESLST LSSTNLAEIS PATSVWFPVN QKTLFAFLSN PSFRHEWDTL  480
TNNTRMEETI RIQKAKRHGN IISLLKIVVS FKQNQIKWGR FCLMFPLIFV SFAKQGNDTL  540
VLQEIWNDAS GAMVVYAPVE TNPMEWVKRG GNSDSVQLLP SGFSIMPDGV PDRKGKSKNG  600
GGGGSLVTFG LQILFSSNPT AVIPQGYVKN VEVLMVHTIG KIKSALRRQT *
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of time of flowering through the photoperiod flowering pathway. May repress FT. {ECO:0000269|PubMed:17189287}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraha.12285s0010.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2435350.0AF243535.1 Arabidopsis thaliana homeodomain-containing transcription factor FWA (FWA) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020873337.10.0homeobox-leucine zipper protein HDG6 isoform X1
SwissprotQ9FVI60.0FWA_ARATH; Homeobox-leucine zipper protein HDG6
TrEMBLB5BQ000.0B5BQ00_9BRAS; Homeodomain-containing transcription factor FWA
STRINGAT4G25530.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM2095355
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G25530.10.0FLOWERING WAGENINGEN
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Rea M, et al.
    Determination of DNA methylation of imprinted genes in Arabidopsis endosperm.
    J Vis Exp, 2011.
    [PMID:21307831]
  3. Nakamura M, et al.
    The role of Arabidopsis thaliana NAR1, a cytosolic iron-sulfur cluster assembly component, in gametophytic gene expression and oxidative stress responses in vegetative tissue.
    New Phytol., 2013. 199(4): p. 925-35
    [PMID:23734982]
  4. Xu Y,Gan ES,He Y,Ito T
    Flowering and genome integrity control by a nuclear matrix protein in Arabidopsis.
    Nucleus, 2013 Jul-Aug. 4(4): p. 274-6
    [PMID:23836195]
  5. Jones AL,Sung S
    Mechanisms underlying epigenetic regulation in Arabidopsis thaliana.
    Integr. Comp. Biol., 2014. 54(1): p. 61-7
    [PMID:24808013]
  6. Buzas DM,Nakamura M,Kinoshita T
    Epigenetic role for the conserved Fe-S cluster biogenesis protein AtDRE2 in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(37): p. 13565-70
    [PMID:25197096]
  7. Bond DM,Baulcombe DC
    Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(3): p. 917-22
    [PMID:25561534]
  8. Li Y, et al.
    An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected].
    PLoS Genet., 2015. 11(1): p. e1004905
    [PMID:25569774]
  9. Sornay E,Forzani C,Forero-Vargas M,Dewitte W,Murray JA
    Activation of CYCD7;1 in the central cell and early endosperm overcomes cell-cycle arrest in the Arabidopsis female gametophyte, and promotes early endosperm and embryo development.
    Plant J., 2015. 84(1): p. 41-55
    [PMID:26261067]
  10. Wang L, et al.
    Tetrahydrofolate Modulates Floral Transition through Epigenetic Silencing.
    Plant Physiol., 2017. 174(2): p. 1274-1284
    [PMID:28450424]
  11. Gallego-Bartolomé J, et al.
    Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain.
    Proc. Natl. Acad. Sci. U.S.A., 2018. 115(9): p. E2125-E2134
    [PMID:29444862]