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Plant Transcription
Factor Database
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Transcription Factor Information
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Basic
Information? help
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| TF ID |
AT4G04890.1 |
| Common Name | PDF2, T1J1.3 |
| Organism |
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| Taxonomic ID |
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| Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
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| Family |
HD-ZIP |
| Protein Properties |
Length: 743aa MW: 81530.1 Da PI: 5.7576 |
| Description |
protodermal factor 2 |
| Gene Model |
|
| Signature Domain? help Back to Top |
 |
| No. |
Domain |
Score |
E-value |
Start |
End |
HMM Start |
HMM End |
| 1 | Homeobox | 61.2 | 1.6e-19 | 63 | 118 | 1 | 56 |
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
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| 2 | START | 215.8 | 1.5e-67 | 253 | 473 | 1 | 206 |
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
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| Gene Ontology ? help Back to Top |
| GO Term |
GO Category |
GO Description |
| GO:0006355 | Biological Process | regulation of transcription, DNA-templated |
| GO:0009845 | Biological Process | seed germination |
| GO:0009913 | Biological Process | epidermal cell differentiation |
| GO:0048497 | Biological Process | maintenance of floral organ identity |
| GO:0048825 | Biological Process | cotyledon development |
| GO:0005634 | Cellular Component | nucleus |
| GO:0003677 | Molecular Function | DNA binding |
| GO:0003700 | Molecular Function | transcription factor activity, sequence-specific DNA binding |
| GO:0005515 | Molecular Function | protein binding |
| GO:0008289 | Molecular Function | lipid binding |
| GO:0043565 | Molecular Function | sequence-specific DNA binding |
| 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
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| Expression --
Description ? help
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| Source |
Description |
| Uniprot | TISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot meristems. {ECO:0000269|PubMed:12505995}. |
| Functional Description ? help
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| Source |
Description |
| TAIR | Encodes 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. |
| UniProt | Probable 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
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- 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] - 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] - 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] - 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]
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| Annotation --
Nucleotide ? help
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| Source |
Hit ID |
E-value |
Description |
| GenBank | AF424560 | 0.0 | AF424560.1 Arabidopsis thaliana AT4g04890/T1J1_3 mRNA, complete cds. |
| GenBank | AY062575 | 0.0 | AY062575.1 Arabidopsis thaliana Unknown protein (At4g04890; T1J1.3) mRNA, complete cds. |
| GenBank | BT000144 | 0.0 | BT000144.1 Arabidopsis thaliana Unknown protein (At4g04890) mRNA, complete cds. |
| Publications
? help Back to Top |
- 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] - Riechmann JL, et al.
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
Science, 2000. 290(5499): p. 2105-10
[PMID:11118137] - 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] - Meinke DW, et al.
A sequence-based map of Arabidopsis genes with mutant phenotypes.
Plant Physiol., 2003. 131(2): p. 409-18
[PMID:12586866] - Yamada K, et al.
Empirical analysis of transcriptional activity in the Arabidopsis genome.
Science, 2003. 302(5646): p. 842-6
[PMID:14593172] - 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] - 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] - 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] - 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] - Arabidopsis Interactome Mapping Consortium
Evidence for network evolution in an Arabidopsis interactome map.
Science, 2011. 333(6042): p. 601-7
[PMID:21798944] - 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] - 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] - Ding Y, et al.
Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
BMC Plant Biol., 2013. 13: p. 229
[PMID:24377444] - 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] - 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] - 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]
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