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Entry version 160 (26 Feb 2020)
Sequence version 1 (01 Nov 1996)
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Protein

Glycerophosphocholine phosphodiesterase GDE1

Gene

GDE1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:4 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 protein 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

Glycerophosphocholine glycerophosphodiesterase responsible for the hydrolysis of intracellular glycerophosphocholine into glycerol-phosphate and choline (PubMed:16141200, PubMed:16172116). The choline is used for phosphatidyl-choline synthesis (PubMed:16141200). Required for utilization of glycerophosphocholine as phosphate source (PubMed:16141200).2 Publications

Miscellaneous

Present with 2300 molecules/cell in log phase SD medium.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

  • glycerophosphocholine phosphodiesterase activity Source: SGD

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 functionHydrolase

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MetaCyc:G3O-34012-MONOMER
YEAST:G3O-34012-MONOMER

Chemistry databases

SwissLipids knowledge resource for lipid biology

More...
SwissLipidsi
SLP:000000074

<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%5Fand%5Ftaxonomy%5Fsection">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:
Glycerophosphocholine phosphodiesterase GDE11 Publication (EC:3.1.4.21 Publication)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:GDE11 Publication
Ordered Locus Names:YPL110C
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 XVI

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YPL110C

Saccharomyces Genome Database

More...
SGDi
S000006031 GDE1

<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

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Affects the glycerophosphocholine metabolism but not the glycerophosphoinositol metabolism (PubMed:16141200).

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002330091 – 1223Glycerophosphocholine phosphodiesterase GDE1Add BLAST1223

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei653PhosphoserineCombined sources1
Modified residuei983PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q02979

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

More...
PaxDbi
Q02979

PRoteomics IDEntifications database

More...
PRIDEi
Q02979

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q02979

<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)

More...
BioGridi
36071, 60 interactors

Database of interacting proteins

More...
DIPi
DIP-8774N

Protein interaction database and analysis system

More...
IntActi
Q02979, 9 interactors

Molecular INTeraction database

More...
MINTi
Q02979

STRING: functional protein association networks

More...
STRINGi
4932.YPL110C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
Q02979 protein

<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%5Fand%5Fdomains%5Fsection">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>Domaini1 – 213SPXPROSITE-ProRule annotationAdd BLAST213
<p>This subsection of the 'Family and Domains' section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati427 – 456ANK 1Add BLAST30
Repeati472 – 502ANK 2Add BLAST31
Repeati504 – 533ANK 3Add BLAST30
Repeati538 – 567ANK 4Add BLAST30
Repeati572 – 601ANK 5Add BLAST30
Repeati605 – 634ANK 6Add BLAST30
Domaini872 – 1217GP-PDEAdd BLAST346

<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

Belongs to the GDE1 family.Curated

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_005444_1_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q02979

KEGG Orthology (KO)

More...
KOi
K18696

Identification of Orthologs from Complete Genome Data

More...
OMAi
HSTQLDT

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.20, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002110 Ankyrin_rpt
IPR020683 Ankyrin_rpt-contain_dom
IPR036770 Ankyrin_rpt-contain_sf
IPR033506 Gde1
IPR030395 GP_PDE_dom
IPR017946 PLC-like_Pdiesterase_TIM-brl
IPR004331 SPX_dom

The PANTHER Classification System

More...
PANTHERi
PTHR22958:SF1 PTHR22958:SF1, 2 hits

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF12796 Ank_2, 1 hit
PF03009 GDPD, 1 hit
PF03105 SPX, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00248 ANK, 7 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF48403 SSF48403, 1 hit
SSF51695 SSF51695, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50297 ANK_REP_REGION, 1 hit
PS50088 ANK_REPEAT, 2 hits
PS51704 GP_PDE, 1 hit
PS51382 SPX, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q02979-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKFGKTFANH RIPEWSSQYV GYKSLKKMIK EITRLQEDIY RAHNKNSYDE
60 70 80 90 100
GRPPTKMRDS SNSAQNYLDS PKIQKLLASF FFAVDRDIEK VDTFYNSQYA
110 120 130 140 150
EYKKRFERLL SSNQFNEIKS TLVVDANKED AVAQTLLTKD TREMNMLLKG
160 170 180 190 200
TSQASRLSYH KDDLIEIQSI LAELRKQFRN LKWYAELNKR AFGKILKKLD
210 220 230 240 250
KKVGTNQQMS TMKTRILPLQ FANDSLITKD LSLLKTIWEQ VTFRINSYER
260 270 280 290 300
VMRSTSPNAN ANDNTEFFKI ICVFIEEDDS KGLIRELTNL YSELSLIPTR
310 320 330 340 350
IMISVLNKAA LSKSLACIDA ILKVIPSLND SEDINRRNFF HHHIIAIGKL
360 370 380 390 400
IRKQEILSRK KKSQPSKYTN SEGEIVTDLR TLHTTLSAPA ESDSITEEEK
410 420 430 440 450
SSACTLSYIL EELPIHLRPC LFQHDNYKRT PLHYSCQYGL SEVTKLIIKL
460 470 480 490 500
MKEWNIWNEI PIDDVSAFGD AESLTPLHLC VLGAHPKTTE VLLQSLDPNV
510 520 530 540 550
KLKSSSLLHL ATEWNNYPLL HVLLSSKRFD INYQDNELHE TPLYLACRLN
560 570 580 590 600
FFEAAVCLLY NGADLEIREK LFGWTAIFVA AAEGFTDIVK LLIANNANFD
610 620 630 640 650
IEDEGGWTPM EHAVLRGHLH IADMVQIRDE LVTHPHSQLN SGSEEKEPLN
660 670 680 690 700
EISAGELNER NENGNGGNKG SLGKLAGPIK SYGHRFLDNN ESLILITLGS
710 720 730 740 750
NDTRNKSPSI SLSSEALAKV IGLETDCALS LVISCNDSID KSSVILDLPL
760 770 780 790 800
DDNVDAVDFK VPFKVDYSHT LYFDIVPTYG TRSLETHNRI DCQKNNNNYV
810 820 830 840 850
MARGVSMLNK SYSSVGVNRS ILNGSVTVPI IANHTLEILG TLKFEYIIIT
860 870 880 890 900
PFEHPQLPLE RTETYWKSLV STRVIGHRGL GKNNPNKSLQ IGENTVESFI
910 920 930 940 950
MAASLGASYV EFDVQLTKDN VPVVYHDFLV AETGVDIPMH ELTLEQFLDL
960 970 980 990 1000
NNADKEHIQR GAGHSPHHVN GADTALQKYR GRSVDDSDVS TLRRAWDLHD
1010 1020 1030 1040 1050
NDPNGKSNNA HWSDNRMRLT KTFKKNNFKG NARGHSIASS FVTLKELFKK
1060 1070 1080 1090 1100
IPANVGFNIE CKFPMLDEAE EEELGQIMME MNHWVDTVLK VVFDNANGRD
1110 1120 1130 1140 1150
IIFSSFHPDI CIMLSLKQPV IPILFLTEGG SEQMADLRAS SLQNGIRFAK
1160 1170 1180 1190 1200
KWNLLGIVSA AAPILKAPRL VQVVKSNGLV CVTYGVDNND PENASIQIEA
1210 1220
GVDAVIVDSV LAIRRGLTKK NEK
Length:1,223
Mass (Da):138,014
Last modified:November 1, 1996 - 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:iC42E74B3CB7FB382
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U43503 Genomic DNA Translation: AAB68251.1
BK006949 Genomic DNA Translation: DAA11323.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S62011

NCBI Reference Sequences

More...
RefSeqi
NP_015215.1, NM_001183924.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YPL110C_mRNA; YPL110C; YPL110C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
855994

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YPL110C

<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
U43503 Genomic DNA Translation: AAB68251.1
BK006949 Genomic DNA Translation: DAA11323.1
PIRiS62011
RefSeqiNP_015215.1, NM_001183924.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

BioGridi36071, 60 interactors
DIPiDIP-8774N
IntActiQ02979, 9 interactors
MINTiQ02979
STRINGi4932.YPL110C

Chemistry databases

SwissLipidsiSLP:000000074

PTM databases

iPTMnetiQ02979

Proteomic databases

MaxQBiQ02979
PaxDbiQ02979
PRIDEiQ02979

Genome annotation databases

EnsemblFungiiYPL110C_mRNA; YPL110C; YPL110C
GeneIDi855994
KEGGisce:YPL110C

Organism-specific databases

EuPathDBiFungiDB:YPL110C
SGDiS000006031 GDE1

Phylogenomic databases

HOGENOMiCLU_005444_1_0_1
InParanoidiQ02979
KOiK18696
OMAiHSTQLDT

Enzyme and pathway databases

BioCyciMetaCyc:G3O-34012-MONOMER
YEAST:G3O-34012-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q02979
RNActiQ02979 protein

Family and domain databases

Gene3Di1.25.40.20, 1 hit
InterProiView protein in InterPro
IPR002110 Ankyrin_rpt
IPR020683 Ankyrin_rpt-contain_dom
IPR036770 Ankyrin_rpt-contain_sf
IPR033506 Gde1
IPR030395 GP_PDE_dom
IPR017946 PLC-like_Pdiesterase_TIM-brl
IPR004331 SPX_dom
PANTHERiPTHR22958:SF1 PTHR22958:SF1, 2 hits
PfamiView protein in Pfam
PF12796 Ank_2, 1 hit
PF03009 GDPD, 1 hit
PF03105 SPX, 1 hit
SMARTiView protein in SMART
SM00248 ANK, 7 hits
SUPFAMiSSF48403 SSF48403, 1 hit
SSF51695 SSF51695, 1 hit
PROSITEiView protein in PROSITE
PS50297 ANK_REP_REGION, 1 hit
PS50088 ANK_REPEAT, 2 hits
PS51704 GP_PDE, 1 hit
PS51382 SPX, 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 nameiGDE1_YEAST
<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: Q02979
Secondary accession number(s): D6W3Q7
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: November 1, 1996
Last modified: February 26, 2020
This is version 160 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 programFungal 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. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names
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