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Entry version 133 (11 Dec 2019)
Sequence version 1 (01 Dec 2001)
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Protein

Homeobox-leucine zipper protein PROTODERMAL FACTOR 2

Gene

PDF2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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 ATML1.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi62 – 121HomeoboxPROSITE-ProRule annotationAdd BLAST60

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding
Biological processDifferentiation, Transcription, Transcription regulation

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
Alternative name(s):
HD-ZIP protein PDF2
Homeodomain transcription factor PDF2
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PDF2
Ordered Locus Names:At4g04890
ORF Names:T1J1.3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiArabidopsis thaliana (Mouse-ear cress)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri3702 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000006548 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 4

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT4G04890

The Arabidopsis Information Resource

More...
TAIRi
locus:2135368 AT4G04890

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003317351 – 743Homeobox-leucine zipper protein PROTODERMAL FACTOR 2Add BLAST743

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q93V99

PRoteomics IDEntifications database

More...
PRIDEi
Q93V99

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q93V99

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Specifically expressed in the layer 1 (L1) of shoot meristems.1 Publication

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q93V99 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q93V99 AT

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
11139, 8 interactors

Protein interaction database and analysis system

More...
IntActi
Q93V99, 3 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT4G04890.1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q93V99

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini244 – 476STARTPROSITE-ProRule annotationAdd BLAST233

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili110 – 192Sequence analysisAdd BLAST83

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Keywords - Domaini

Coiled coil, Homeobox

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG410IIN5 Eukaryota
ENOG411107H LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000243256

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q93V99

KEGG Orthology (KO)

More...
KOi
K09338

Identification of Orthologs from Complete Genome Data

More...
OMAi
PVAPYGV

Database of Orthologous Groups

More...
OrthoDBi
279393at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q93V99

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00086 homeodomain, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.530.20, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR042160 GLABRA2/ANL2/PDF2/ATML1-like
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR023393 START-like_dom_sf
IPR002913 START_lipid-bd_dom

The PANTHER Classification System

More...
PANTHERi
PTHR45654 PTHR45654, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00046 Homeodomain, 1 hit
PF01852 START, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00389 HOX, 1 hit
SM00234 START, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46689 SSF46689, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS50848 START, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q93V99-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG TEVTTENPSG
60 70 80 90 100
EELQDPSQRP NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN
110 120 130 140 150
LEPLQVKFWF QNKRTQMKAQ SERHENQILK SDNDKLRAEN NRYKEALSNA
160 170 180 190 200
TCPNCGGPAA IGEMSFDEQH LRIENARLRE EIDRISAIAA KYVGKPLGSS
210 220 230 240 250
FAPLAIHAPS RSLDLEVGNF GNQTGFVGEM YGTGDILRSV SIPSETDKPI
260 270 280 290 300
IVELAVAAME ELVRMAQTGD PLWLSTDNSV EILNEEEYFR TFPRGIGPKP
310 320 330 340 350
LGLRSEASRQ SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST
360 370 380 390 400
GVAGNYNGAL QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL
410 420 430 440 450
DSLRPSTPIL RTRRRPSGCL IQELPNGYSK VTWIEHMEVD DRSVHNMYKP
460 470 480 490 500
LVQSGLAFGA KRWVATLERQ CERLASSMAS NIPGDLSVIT SPEGRKSMLK
510 520 530 540 550
LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM DDPGRPPGIV
560 570 580 590 600
LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP
610 620 630 640 650
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG
660 670 680 690 700
GDPDYVALLP SGFAILPDGS VGGGDGNQHQ EMVSTTSSGS CGGSLLTVAF
710 720 730 740
QILVDSVPTA KLSLGSVATV NSLIKCTVER IKAAVSCDVG GGA
Length:743
Mass (Da):81,530
Last modified:December 1, 2001 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDF305491CC69EF8C
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAD17342 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB81031 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AB056455 Genomic DNA Translation: BAB58961.1
AF128393 Genomic DNA Translation: AAD17342.1 Sequence problems.
AL161502 Genomic DNA Translation: CAB81031.1 Different initiation.
CP002687 Genomic DNA Translation: AEE82438.1
CP002687 Genomic DNA Translation: ANM67658.1
AF424560 mRNA Translation: AAL11554.1
AY062575 mRNA Translation: AAL32653.1
BT000144 mRNA Translation: AAN15463.1

Protein sequence database of the Protein Information Resource

More...
PIRi
E85061

NCBI Reference Sequences

More...
RefSeqi
NP_001329475.1, NM_001340517.1
NP_567274.1, NM_116727.4

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G04890.1; AT4G04890.1; AT4G04890
AT4G04890.2; AT4G04890.2; AT4G04890

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
825828

Gramene; a comparative resource for plants

More...
Gramenei
AT4G04890.1; AT4G04890.1; AT4G04890
AT4G04890.2; AT4G04890.2; AT4G04890

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G04890

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB056455 Genomic DNA Translation: BAB58961.1
AF128393 Genomic DNA Translation: AAD17342.1 Sequence problems.
AL161502 Genomic DNA Translation: CAB81031.1 Different initiation.
CP002687 Genomic DNA Translation: AEE82438.1
CP002687 Genomic DNA Translation: ANM67658.1
AF424560 mRNA Translation: AAL11554.1
AY062575 mRNA Translation: AAL32653.1
BT000144 mRNA Translation: AAN15463.1
PIRiE85061
RefSeqiNP_001329475.1, NM_001340517.1
NP_567274.1, NM_116727.4

3D structure databases

SMRiQ93V99
ModBaseiSearch...

Protein-protein interaction databases

BioGridi11139, 8 interactors
IntActiQ93V99, 3 interactors
STRINGi3702.AT4G04890.1

PTM databases

iPTMnetiQ93V99

Proteomic databases

PaxDbiQ93V99
PRIDEiQ93V99

Genome annotation databases

EnsemblPlantsiAT4G04890.1; AT4G04890.1; AT4G04890
AT4G04890.2; AT4G04890.2; AT4G04890
GeneIDi825828
GrameneiAT4G04890.1; AT4G04890.1; AT4G04890
AT4G04890.2; AT4G04890.2; AT4G04890
KEGGiath:AT4G04890

Organism-specific databases

AraportiAT4G04890
TAIRilocus:2135368 AT4G04890

Phylogenomic databases

eggNOGiENOG410IIN5 Eukaryota
ENOG411107H LUCA
HOGENOMiHOG000243256
InParanoidiQ93V99
KOiK09338
OMAiPVAPYGV
OrthoDBi279393at2759
PhylomeDBiQ93V99

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q93V99

Gene expression databases

ExpressionAtlasiQ93V99 baseline and differential
GenevisibleiQ93V99 AT

Family and domain databases

CDDicd00086 homeodomain, 1 hit
Gene3Di3.30.530.20, 1 hit
InterProiView protein in InterPro
IPR042160 GLABRA2/ANL2/PDF2/ATML1-like
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR023393 START-like_dom_sf
IPR002913 START_lipid-bd_dom
PANTHERiPTHR45654 PTHR45654, 1 hit
PfamiView protein in Pfam
PF00046 Homeodomain, 1 hit
PF01852 START, 1 hit
SMARTiView protein in SMART
SM00389 HOX, 1 hit
SM00234 START, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
PROSITEiView protein in PROSITE
PS00027 HOMEOBOX_1, 1 hit
PS50071 HOMEOBOX_2, 1 hit
PS50848 START, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPDF2_ARATH
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q93V99
Secondary accession number(s): Q9M0Z0, Q9ZPH7
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: December 1, 2001
Last modified: December 11, 2019
This is version 133 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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