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 Cagra.23907s0014.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family HD-ZIP
Protein Properties Length: 642aa    MW: 71606.1 Da    PI: 5.016
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.23907s0014.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox55.59.7e-184999656
                          S--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
              Homeobox  6 tftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                          ++t+ q++eLe+++e n+ p+ ++r eL ++l+L+ rqVk+WFqN+R +ek
  Cagra.23907s0014.1.p 49 RHTAFQIQELETFYEGNPLPTSDQRNELGQRLNLEARQVKFWFQNKRSQEK 99
                          56899*******************************************998 PP
2START1433e-451933981206
                           HHHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT. CS
                 START   1 elaeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg. 88 
                           ela++a++el ++ + ++p+W+++     +d+v   +     + +e +r +g+v m + +lv++l+d++ +W   +a  +++ v s + 
  Cagra.23907s0014.1.p 193 ELANTAMDELKALGERNCPFWTLDL---RNDIVGPPE-----CAVESSRCIGLVRMGSSTLVKTLMDTG-KWVDVFA--SIVHVASAQk 270
                           57899********************...444444444.....8**************************.*******..5555555555 PP

                           ...........EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEE CS
                 START  89 ...........galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvt 165
                                      g lq+++ae+q++splvp R ++f+Ry++ lg+g+wv+vd  +d+ ++p+   ++  +++lpSg++i++++ng+s+vt
  Cagra.23907s0014.1.p 271 lirptysgarsGSLQQIQAEFQVMSPLVPkRQVTFLRYCKDLGDGSWVVVD-VTDPAEYPT-FFPYGASNRLPSGLIIRDMANGYSEVT 357
                           55555777*******************************************.355666666.89************************* PP

                           EEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                 START 166 wvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                           w+e+++++++++h+l+++l+ sg+  gak+w+ tlqr+ce+
  Cagra.23907s0014.1.p 358 WIEQAEYNKNHIHQLYQPLIASGIGLGAKRWLTTLQRYCES 398
                           ***************************************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.1E-163599IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.606.0E-1839104IPR009057Homeodomain-like
PROSITE profilePS5007115.83941101IPR001356Homeobox domain
SMARTSM003893.3E-1343105IPR001356Homeobox domain
CDDcd000865.90E-144599No hitNo description
PfamPF000463.6E-154999IPR001356Homeobox domain
PROSITE profilePS5084835.336184401IPR002913START domain
SuperFamilySSF559619.01E-23187399No hitNo description
CDDcd088753.13E-77189397No hitNo description
SMARTSM002343.8E-31193398IPR002913START domain
PfamPF018525.1E-41193398IPR002913START domain
SuperFamilySSF559619.61E-17420633No 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: 642 aa     Download sequence    Send to blast
MDGQGDFNEF GNIFKTNLGS AEDEESNIID AMNCDNDGDD GGRMRRSFRH TAFQIQELET  60
FYEGNPLPTS DQRNELGQRL NLEARQVKFW FQNKRSQEKV NKERLENICL IENNERLLGA  120
QDELRMLQIS DYGDVDYKID KYSNFPFNAL QVQVTAPEQL PSSSSNPIRN ATPQLDSGRG  180
YISAKKDEAK LLELANTAMD ELKALGERNC PFWTLDLRND IVGPPECAVE SSRCIGLVRM  240
GSSTLVKTLM DTGKWVDVFA SIVHVASAQK LIRPTYSGAR SGSLQQIQAE FQVMSPLVPK  300
RQVTFLRYCK DLGDGSWVVV DVTDPAEYPT FFPYGASNRL PSGLIIRDMA NGYSEVTWIE  360
QAEYNKNHIH QLYQPLIASG IGLGAKRWLT TLQRYCESLS TLSATNMGEI IPGMSAKGAN  420
ELMKLTERMT RNYYTGITSS TVGKWEMIEV ENVAQNMRFM TRKSLNEPGE YTGIVLSAAI  480
SVWFPVNQRT LFAFLNHLGS RHEWDSLTLT SMEEIFRIQK ANRHENTISL LRVIGDENDM  540
LVLQEVWNDA SGAVLVYAPV ETSSIEAVNR GENSNYVPLL PSGFSIVPDG STGGGCLLTL  600
GLQILASTNP TALLTQGFVK IVEGLMLHTI DKIKSALHKQ P*
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
PlantRegMapCagra.23907s0014.1.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
GenBankAB3678170.0AB367817.1 Turritis glabra FWA mRNA for homeodomain-containing transcription factor FWA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006285631.10.0homeobox-leucine zipper protein HDG6 isoform X1
SwissprotQ9FVI60.0FWA_ARATH; Homeobox-leucine zipper protein HDG6
TrEMBLR0GNU90.0R0GNU9_9BRAS; Uncharacterized protein
STRINGCagra.23907s0014.1.p0.0(Capsella grandiflora)
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]