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 Carubv10007084m
Common NameCARUB_v10007084mg
Organism
Capsella rubella
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: 627aa    MW: 69805.1 Da    PI: 5.1432
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10007084mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox55.59.4e-184999656
                     S--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
         Homeobox  6 tftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                     ++t+ q++eLe+++e n+ p+ ++r eL ++l+L+ rqVk+WFqN+R +ek
  Carubv10007084m 49 RHTAFQIQELETFYEGNPLPTSDQRNELGQRLNLEARQVKFWFQNKRSQEK 99
                     56899*******************************************998 PP
2START139.92.5e-441783831206
                      HHHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT...... CS
            START   1 elaeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg...... 88 
                      ela++a++el ++ + ++p+W+++     + + +  +    ++  e +r +g+v m + +lv++l+d++ +W   +a  +++ v s +      
  Carubv10007084m 178 ELANTAMDELKALGERNCPFWTLDL----RNDIVGPP----GCAAESSRCIGLVRMGSSTLVKTLMDTG-KWVDVFA--SIVHVASAQklirpt 260
                      57899999999999999*****999....55555555....389*************************.*******..555555555555555 PP

                      ......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SS CS
            START  89 ......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgr 175
                            g lq+++ae+q++splvp R ++f+Ry++ lg+g+wv+vd  +d+ ++p+   ++  +++lpSg++i++++ng+s+vtw+e+++++++
  Carubv10007084m 261 ysgarsGSLQQIQAEFQVMSPLVPkRQVTFLRYCKDLGDGSWVVVD-VTDPAEYPT-FFPYGASNRLPSGLIIRDMANGYSEVTWIEQAEYNKN 352
                      777*******************************************.355666666.89*********************************** PP

                      XXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
            START 176 lphwllrslvksglaegaktwvatlqrqcek 206
                      ++h+l+++l+ sg+  gak+w+ tlqr+ce+
  Carubv10007084m 353 HIHQLYQPLIASGIGLGAKRWLTTLQRYCES 383
                      *****************************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.97E-163599IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.608.3E-1839102IPR009057Homeodomain-like
PROSITE profilePS5007115.83941101IPR001356Homeobox domain
SMARTSM003893.8E-1343105IPR001356Homeobox domain
CDDcd000865.38E-144599No hitNo description
PfamPF000463.5E-154999IPR001356Homeobox domain
PROSITE profilePS5084835.507169386IPR002913START domain
SuperFamilySSF559612.09E-22172384No hitNo description
CDDcd088751.10E-76174382No hitNo description
PfamPF018524.9E-40178383IPR002913START domain
SMARTSM002341.0E-29178383IPR002913START domain
SuperFamilySSF559611.51E-15405615No 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: 627 aa     Download sequence    Send to blast
MDGQGDFNEF GNIFKTILGS TEDEESNIID AMNCDNDGDD GGRMRRSFRH TAFQIQELET  60
FYEGNPLPTS DQRNELGQRL NLEARQVKFW FQNKRSQEKV NKECLENICL IENNERLLEA  120
QDELRMLQIS NYGDVDYKAT APEQLPSSSS NPIRNATPQL DSGRGYISAK KDEAKLLELA  180
NTAMDELKAL GERNCPFWTL DLRNDIVGPP GCAAESSRCI GLVRMGSSTL VKTLMDTGKW  240
VDVFASIVHV ASAQKLIRPT YSGARSGSLQ QIQAEFQVMS PLVPKRQVTF LRYCKDLGDG  300
SWVVVDVTDP AEYPTFFPYG ASNRLPSGLI IRDMANGYSE VTWIEQAEYN KNHIHQLYQP  360
LIASGIGLGA KRWLTTLQRY CESLSTLSAT NMGEIIPGMS AKGANELMKL TKRMTRNYYT  420
GMTSSTVGKW EMIEVENVAQ NMRFMTRKSL NEPGEYTGIV LSAAISVWFP VNQRTLFAFL  480
NHLGSRHEWD TLTLTSMEEI FRIQKANRHE NTISLLRVIG DENDMLVLQE VWNDASGAVL  540
VYAPVETSSI EAVNRGENSN YVPLLPSGFS IVPDGSTGGG CLLTLGLQIL ASTNPTAQLT  600
QGFVKIVEGL MLHTIDKIKS ALHKQP*
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
PlantRegMapCarubv10007084m
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_006285631.10.0homeobox-leucine zipper protein HDG6 isoform X1
SwissprotQ9FVI60.0FWA_ARATH; Homeobox-leucine zipper protein HDG6
TrEMBLR0GNU90.0R0GNU9_9BRAS; Uncharacterized protein
STRINGXP_006285631.10.0(Capsella rubella)
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]