PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G04890.1
Common NamePDF2, T1J1.3
Organism
Arabidopsis thaliana
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: 743aa    MW: 81530.1 Da    PI: 5.7576
Description protodermal factor 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G04890.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.21.6e-1963118156
                  TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
     Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                  +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l+L+  qVk+WFqN+R+++k
  AT4G04890.1  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLNLEPLQVKFWFQNKRTQMK 118
                  688999***********************************************998 PP
2START215.81.5e-672534731206
                  HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEEEC CS
        START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetlevis 86 
                  ela +a++elv++a+ ++p+W +     e++n++e+ ++f+++ +      ++ea+r s+vv+m++ +lve+l+d++ qW+  +     +a tlev+s
  AT4G04890.1 253 ELAVAAMEELVRMAQTGDPLWLSTDnsvEILNEEEYFRTFPRGIGpkplgLRSEASRQSAVVIMNHINLVEILMDVN-QWSCVFSgivsRALTLEVLS 349
                  57899*****************998899**************999********************************.******************** PP

                  TT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXX CS
        START  87 sg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgrlp 177
                  +g      galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds ++ +   ++ R +++pSg+li++++ng+skvtw+eh+++++r++
  AT4G04890.1 350 TGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPST---PILRTRRRPSGCLIQELPNGYSKVTWIEHMEVDDRSV 444
                  *******************************************************976...7************************************ PP

                  HHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
        START 178 hwllrslvksglaegaktwvatlqrqcek 206
                  h+++++lv+sgla+gak+wvatl+rqce+
  AT4G04890.1 445 HNMYKPLVQSGLAFGAKRWVATLERQCER 473
                  ***************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.608.4E-2444118IPR009057Homeodomain-like
SuperFamilySSF466896.68E-1949120IPR009057Homeodomain-like
PROSITE profilePS5007116.95760120IPR001356Homeobox domain
SMARTSM003891.0E-1761124IPR001356Homeobox domain
PfamPF000463.7E-1763118IPR001356Homeobox domain
CDDcd000863.58E-1863121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084845.211244476IPR002913START domain
SuperFamilySSF559612.47E-35246475No hitNo description
CDDcd088759.01E-125248472No hitNo description
SMARTSM002343.6E-77253473IPR002913START domain
PfamPF018526.6E-57254473IPR002913START domain
Gene3DG3DSA:3.30.530.201.9E-7349473IPR023393START-like domain
SuperFamilySSF559616.53E-26492732No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009845Biological Processseed germination
GO:0009913Biological Processepidermal cell differentiation
GO:0048497Biological Processmaintenance of floral organ identity
GO:0048825Biological Processcotyledon development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000017anatomyvascular leaf primordium
PO:0000037anatomyshoot apex
PO:0000229anatomyflower meristem
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0006210anatomyprotoderm
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009020anatomymeristem L1 layer
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001180developmental stageplant proembryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 743 aa     Download sequence    Send to blast
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG TEVTTENPSG EELQDPSQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN LEPLQVKFWF QNKRTQMKAQ  120
SERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPLGSS FAPLAIHAPS RSLDLEVGNF GNQTGFVGEM YGTGDILRSV  240
SIPSETDKPI IVELAVAAME ELVRMAQTGD PLWLSTDNSV EILNEEEYFR TFPRGIGPKP  300
LGLRSEASRQ SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL  360
QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPSTPIL RTRRRPSGCL  420
IQELPNGYSK VTWIEHMEVD DRSVHNMYKP LVQSGLAFGA KRWVATLERQ CERLASSMAS  480
NIPGDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM  540
DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP  600
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG GDPDYVALLP  660
SGFAILPDGS VGGGDGNQHQ EMVSTTSSGS CGGSLLTVAF QILVDSVPTA KLSLGSVATV  720
NSLIKCTVER IKAAVSCDVG GGA
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.40470.0floral meristem| flower| leaf| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1865115350.0
Genevisible255277_at0.0
Expression AtlasAT4G04890-
AtGenExpressAT4G04890-
ATTED-IIAT4G04890-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot meristems. {ECO:0000269|PubMed:12505995}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a homeodomain protein that is expressed in the LI layer of the vegetative, floral and inflorescence meristems. Binds to the L1 box promoter element which is required in some proteins for L1 specific expression.
UniProtProbable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1. {ECO:0000269|PubMed:12505995}.
Function -- GeneRIF ? help Back to Top
  1. ACR4 positively affects the expression of ATML1 and PDF2 in seedlings. In contrast, ATML1- and PDF2-containing complexes directly and negatively affect both their own expression and that of ACR4.
    [PMID: 24147836]
  2. The allele-specific effect caused by pdf2-1, which carries a T-DNA in a steroidogenic acute regulatory protein-related lipid transfer (START) domain-encoding region, suggests the importance of the START domain in proper function of HD-ZIP IV proteins.
    [PMID: 24390006]
  3. Upon seed imbibition, increased Gibberellin (GA)levels reduce DELLA protein abundance and release ATML1/PDF2 to activate L1 box gene expression, thus enhancing germination potential.
    [PMID: 24989044]
  4. These results indicate that ATML1 and PDF2 act redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development.
    [PMID: 25766904]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G04890.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G04890, AT4G21750, AT1G14920, AT1G79430
IntActSearch Q93V99
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G04890
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4245600.0AF424560.1 Arabidopsis thaliana AT4g04890/T1J1_3 mRNA, complete cds.
GenBankAY0625750.0AY062575.1 Arabidopsis thaliana Unknown protein (At4g04890; T1J1.3) mRNA, complete cds.
GenBankBT0001440.0BT000144.1 Arabidopsis thaliana Unknown protein (At4g04890) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001329475.10.0protodermal factor 2
RefseqNP_567274.10.0protodermal factor 2
SwissprotQ93V990.0PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBLA0A178V5B80.0A0A178V5B8_ARATH; PDF2
STRINGAT4G04890.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM49128149
Representative plantOGRP14515136
Publications ? help Back to Top
  1. Tavares R,Aubourg S,Lecharny A,Kreis M
    Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.
    Plant Mol. Biol., 2000. 42(5): p. 703-17
    [PMID:10809443]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Abe M,Katsumata H,Komeda Y,Takahashi T
    Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis.
    Development, 2003. 130(4): p. 635-43
    [PMID:12505995]
  4. Meinke DW, et al.
    A sequence-based map of Arabidopsis genes with mutant phenotypes.
    Plant Physiol., 2003. 131(2): p. 409-18
    [PMID:12586866]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. 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]
  7. Nakamura M, et al.
    Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis.
    Plant Physiol., 2006. 141(4): p. 1363-75
    [PMID:16778018]
  8. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  9. Lilly ST,Drummond RS,Pearson MN,MacDiarmid RM
    Identification and validation of reference genes for normalization of transcripts from virus-infected Arabidopsis thaliana.
    Mol. Plant Microbe Interact., 2011. 24(3): p. 294-304
    [PMID:21091160]
  10. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  11. Kamata N,Okada H,Komeda Y,Takahashi T
    Mutations in epidermis-specific HD-ZIP IV genes affect floral organ identity in Arabidopsis thaliana.
    Plant J., 2013. 75(3): p. 430-40
    [PMID:23590515]
  12. San-Bento R,Farcot E,Galletti R,Creff A,Ingram G
    Epidermal identity is maintained by cell-cell communication via a universally active feedback loop in Arabidopsis thaliana.
    Plant J., 2014. 77(1): p. 46-58
    [PMID:24147836]
  13. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  14. Kamata N,Sugihara A,Komeda Y,Takahashi T
    Allele-specific effects of PDF2 on floral morphology in Arabidopsis thaliana.
    Plant Signal Behav, 2013. 8(12): p. e27417
    [PMID:24390006]
  15. Rombol
    Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element.
    Plant Cell, 2014. 26(7): p. 2905-19
    [PMID:24989044]
  16. Ogawa E, et al.
    ATML1 and PDF2 Play a Redundant and Essential Role in Arabidopsis Embryo Development.
    Plant Cell Physiol., 2015. 56(6): p. 1183-92
    [PMID:25766904]