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Gene Dmel\zen

General Information
Symbol	Dmel\zen	Species	D. melanogaster
Name	zerknullt	Annotation symbol	CG1046
Feature type	protein_coding_gene	FlyBase ID	FBgn0004053
Gene Model Status	Current	Stock availability	17 publicly available
Also Known As	z1
Genomic Location
Chromosome (arm)	3R	Recombination map	3-47.5
Cytogenetic map	84A5-84A5	Sequence location	3R:2,578,586..2,579,916 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene zerknullt is referred to in FlyBase by the symbol Dmel\zen (CG1046, FBgn0004053). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: sequence-specific DNA binding; sequence-specific distal enhancer binding RNA polymerase II transcription factor activity. There is experimental evidence that it is involved in the biological process: positive regulation of transcription from RNA polymerase II promoter; compound eye development; negative regulation of gene expression. 30 alleles are reported. The phenotypes of these alleles are annotated with: embryonic optic lobe primordium; embryonic head; cuticle; extended germ band embryo; optic lobe; presumptive embryonic/larval central nervous system; denticle belt. It has one annotated transcript and one annotated polypeptide. Protein features are: Homeobox; Homeobox, conserved site; Homeobox, eukaryotic; Homeodomain-like; Homeodomain-related. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages. Summary of FlyAtlas Anatomical Expression Data: No expression detected in any larval or adult organs/tissues. Comments on Affy2 ProbeSet: ProbeSet 1637961_at completely aligns to an exonic region common to each of the 2 FlyBase-annotated transcript isoforms of zen. Gene sequence location is 3R:2578586..2579916.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	zen: zerknullt Null mutations result in embryonic lethality and the loss of several dorsally derived embryonic structures, including the amnioserosa, optic lobe, and dorsal ridge. These animals also fail to fully extend their germ bands and go through the process of head involution. The name for the locus derives from the characteristic "wrinkled" appearance of the germ band seen in the SEM at the time of normal germ-band retraction. Hypomorphic mutations result in the absence of dorsal structures but do undergo normal gastrulation movements. A temperature-sensitive allele has been used to define the time of zen+ action between 2 and 4 hours of embryogenesis, just prior to and overlapping the earliest observable morphogenic defects. X-ray induced somatic clones have further shown that zen+ function is unnecessary for postembryonic development. The RNA product of zen is first detected at about 2 hours of development during the eleventh to twelfth cell cycle of the syncytial blastoderm. At this early stage the RNA is found on the dorsal surface of the embryo extending around the anterior and posterior poles. As cellularization proceeds and the early events of gastrulation begin, the RNA becomes restricted to a mid-dorsal stripe of cells. These cells have been fate mapped and give rise to the amnioserosa and the lobes in the dorsal posterior of the embryonic head, i.e., the structures absent in zen- animals. The time of appearance of zen RNA also correlates nicely with the temperature-sensitive-period data obtained using the conditional allele. Antisera to the zen protein product has been used to follow its accumulation pattern, and this analysis agrees with and expands the in situ results. The protein is located in the nuclei of cells expressing the gene and at cellular blastoderm is found in a mid-dorsal stripe seven cells wide and seventy cells in length. During gastrulation these cells eventually give rise to the amnioserosa, the optic lobe, and dorsal ridge; these structures continue to show zen protein accumulation until the end of germ-band extension at about 4 to 6 hours of development. This end point also correlates well with the end of the temperature-sensitive period of the conditional allele. The spatial pattern of zen expression has been shown to be dependent on the products of several of the maternally expressed genes which specify the anterior-posterior and dorsal-ventral polarity of the embryo, and zen would appear to lie near the end of the axis-determining pathway.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2012_01	Sequence features HFA12632 BKN33335 References Kazemian et al., 2010, PLoS Biol. 8(8): Controlled Vocabulary Terms positive regulation of transcription from RNA polymerase II promoter negative regulation of gene expression sequence-specific distal enhancer binding RNA polymerase II transcription factor activity
FB2011_10	References Gurunathan et al., 2004, BMC Bioinformatics 5: 202
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 84A5-84A5   Limits computationally determined from genome sequence between P{PZ}pb04498 and P{lacW}l(3)L2100L2100
Experimentally Determined Cytological Location
Cytogenetic map Notes References 84A-84B   (determined by in situ hybridisation)   (Rushlow et al., 1987) 84B1-84B2   (determined by in situ hybridisation)   (Doyle et al., 1986)
Experimentally Determined Recombination Data
Location	3-47.5
Left of (cM)	bcd
Right of (cM)	pb
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\zen for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) zen-RA FBtr0081670  NM_057445   1267   353
Additional Transcript Data & Comments
Reported size (kB)	1.3 (northern blot) (Doyle et al., 1986, Rushlow et al., 1987)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein zen-PA   FBpp0081170   39.3   353   9.58     NP_476793   AAF54087
Additional Polypeptide Data & Comments
Reported size (kDa)	353 (aa); 39 (kD predicted) (Rushlow et al., 1987)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) Homeobox, eukaryotic (IPR020479)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014297 AAF54087   AC002512   AE001572 AAD19800   BT028847   GH941925   GH949582   GH949587   GH953358   GH970975   GH974384   GH984096   L18923   S78213   X68347 CAA48416
UniProtKB/Swiss-Prot	P09089
UniProtKB/TrEMBL
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References protein binding site FBsf0000159897 3R:2,581,220..2,581,229 comment=DL_binding_site_ZD1; one of several fragments within the VRE bound by dl protein evidence=experimental bound_moiety=dl-P* bound_moiety=dl-XP (Ip et al., 1991, Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000161124 3R:2,581,202..2,581,214 comment=GC2 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000159899 3R:2,581,253..2,581,265 comment=GC1 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000159898 3R:2,581,238..2,581,250 comment=AT1 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000159896 3R:2,581,183..2,581,197 comment=AT2 evidence=experimental bound_moiety=ct-P* bound_moiety=retn-P* (Jiang et al., 1993, Bergman et al., 2004, Valentine et al., 1998) protein binding site FBsf0000159895 3R:2,581,170..2,581,180 evidence=experimental comment=DL_binding_site_ZD2; one of several fragments within the VRE bound by dl protein bound_moiety=dl-P* bound_moiety=dl-XP (Jiang et al., 1993, Ip et al., 1991, Bergman et al., 2004) protein binding site FBsf0000159894 3R:2,581,139..2,581,158 evidence=experimental comment=AT3/GC3 comment=ct and retn proteins interact with a TATTGAT element found in zen AT2 and AT3 (Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000159893 3R:2,581,102..2,581,111 comment=DL_binding_site_ZD3; one of several fragments within the VRE bound by dl protein evidence=experimental bound_moiety=dl-P* bound_moiety=dl-XP (Ip et al., 1991, Jiang et al., 1993, Bergman et al., 2004) protein binding site FBsf0000160367 3R:2,580,333..2,580,344 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160368 3R:2,580,283..2,580,295 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160369 3R:2,579,958..2,579,970 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160370 3R:2,580,553..2,580,568 bound_moiety=brk-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160371 3R:2,580,148..2,580,167 evidence=experimental bound_moiety=Mad-XP (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160372 3R:2,580,464..2,580,492 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160373 3R:2,580,045..2,580,072 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160374 3R:2,580,147..2,580,160 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160375 3R:2,580,199..2,580,218 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160376 3R:2,580,310..2,580,324 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160377 3R:2,580,196..2,580,208 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160378 3R:2,580,051..2,580,066 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site FBsf0000160379 3R:2,579,983..2,579,995 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160380 3R:2,580,282..2,580,294 bound_moiety=brk-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160381 3R:2,581,266..2,581,278 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site FBsf0000160382 3R:2,581,252..2,581,271 bound_moiety=grh-XP evidence=experimental (Bergman et al., 2004, Huang et al., 1995) protein binding site FBsf0000160383 3R:2,581,266..2,581,277 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) regulatory region FBsf0000161213 3R:2,580,903..2,581,527 comment=ventral response element (VRE) comment=position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental linked_to=XbaI-HindIII_rfrag (Jiang et al., 1993) regulatory region FBsf0000161214 3R:2,581,086..2,581,277 comment=minimal_VRE comment=Position of restriction fragment on reference sequence inferred by FlyBase curator. evidence=experimental linked_to=NarI-XmnI_rfrag (Jiang et al., 1993) regulatory region FBsf0000161215 3R:2,581,264..2,581,270 comment=DRE evidence=experimental (Huang et al., 1995) regulatory region FBsf0000161188 3R:2,580,209..2,580,591 linked_to=EcoRI-AccI_rfrag comment=dorsal activation element required for maintaining high levels of expression on dorsal surface; position of restriction fragment on reference sequence inferred by FlyBase curator evidence=experimental (Doyle et al., 1989)
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 5 -- 6   amnioserosa anlage in statu nascendi   (Martinho et al., 2004) embryonic stage 6 -- 7   amnioserosa   (Podos et al., 2001) amnioserosa primordium   (Podos et al., 2001) Comment:NOT hindgut anlage embryonic cycle 14   organism | anterior & dorsal & posterior   (Rushlow et al., 1987) Comment:anterior and posterior poles and dorsal surface of embryo organism | dorsal   (Tatei and Levine, 1995) extended germ band stage   dorsal ectoderm | restricted   (Rushlow et al., 1987) pole cell | restricted   (Rushlow et al., 1987) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Rushlow et al., 1987) dorsal ectoderm   (Doyle et al., 1986) embryonic stage 3     (Doyle et al., 1986) embryonic stage 4   dorsal ectoderm   (Doyle et al., 1986) embryonic stage 4 -- 6     (Doyle et al., 1986) gastrula stage   organism | dorsal   (Rushlow et al., 1987) embryonic stage 7 -- 10   dorsal ectoderm | restricted   (Doyle et al., 1986) radioisotope in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4 -- 12   pole cell   (Doyle et al., 1989) embryonic cycle 12 -- embryonic cycle 13   organism | dorsal   (Doyle et al., 1989) Comment:includes anterior and posterior pole embryonic stage 5 -- 6   organism | dorsal   (Doyle et al., 1989) embryonic stage 12   amnioserosa   (Doyle et al., 1989)
Additional Descriptive Data
	The zen-RA transcripts are detected along the dorsal surface in embryos following the formation of the syncytial blastoderm. Following gastrulation, the expression of zen-RA is limited to a 5-6 cell wide stripe along the dorsal surface, and is not detected in the posterior 20% of the embryo. (Doyle et al., 1986) Northern analysis of RNA from 0-24 hour embryos indicate that zen transcript is expressed in early embryos, and that expression peaks at 2-3 hours of embryogenesis. Using radioactive in situ hybridization, zen expression is detected in the dorsal surface and the anterior and posterior poles of embryonic cycle 14 embryos. By gastrulation, zen expression is restricted to the dorsal surface. During germ band elongation, zen transcript is detected in the amnioserosa and a region of the dorsal ectoderm corresponding to the presumptive optic lobe, and in a subset of pole cells within the posterior midgut invagination. (Rushlow et al., 1987) Reporter constructs with deletions of 1.6 kb of zen upstream region driving lacZ expression demonstrate that a ventral repression element lies at about -1.2 to -1.4. (Doyle et al., 1989)
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
immunolocalization Stage Tissue/Position (including subcellular localization) Reference embryonic stage 3 -- 11   dorsal ectoderm | restricted   (Rushlow et al., 1987)
Additional Descriptive Data
	Just prior to cellularization, zen protein is detected in the dorsal ectoderm. In later stages, during gastrulation, zen protein expression is resticted to a narrow dorsal stripe. (Rushlow et al., 1987)
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0004053    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0004053 Very low expression bin max Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of no expression detected. Peak expression observed within 00-06 hour embryonic stages. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0004053 expression level Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (546) embryo 02-04hr  (4209) embryo 04-06hr  (193) embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day  (114) adult female 30day  (108) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr  (4209) embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0004053 expression level Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (546) embryo 02-04hr  (4209) embryo 04-06hr  (193) embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day  114 adult female 30day  108 Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr  (4209) embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    546 embryo 02-04hr    4209 embryo 04-06hr    193 embryo 06-08hr    31 embryo 08-10hr    47 embryo 10-12hr    25 embryo 12-14hr    23 embryo 14-16hr    25 embryo 16-18hr    15 embryo 18-20hr    39 embryo 20-22hr    16 embryo 22-24hr    31 larva L1    0 larva L2    1 larva L3 12hr old    0 larva L3 puffstage 1-2    0 larva L3 puffstage 3-6    1 larva L3 puffstage 7-9    1 white prepupae new    1 white prepupae 12hr    7 white prepupae 24hr    4 pupae 2d postWPP    11 pupae 3d postWPP    4 pupae 4d postWPP    8 adult male 01day    5 adult male 05day    4 adult male 30day    7 adult female 01day    85 adult female 05day    114 adult female 30day    108 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     FlyAtlas Anatomical Expression Data for FBgn0004053    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0004053 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: No expression detected in any larval or adult organs/tissues. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (1000 - 25000) Linear, scaled to maximum FBgn0004053 expression level Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0004053 expression level Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    3.375 Larval Midgut    1.6 Larval Hindgut    1 Larval Malpighian Tubules    2.8 Larval Fat Body    2.1 Larval Salivary Gland    2.7 Larval Trachea    3.275 Larval Carcass    2.2 Adult Head    3.2 Adult Eye    3.15 Adult Brain    4.4 Adult Thoracic-Abdominal Ganglion    2.1 Adult Crop    4.1 Adult Midgut    2 Adult Hindgut    1.2 Adult Malpighian Tubules    3.3 Adult Fat Body    6.2 Adult Salivary Gland    4.9 Adult Heart    2.6 Adult VirginFemale Spermatheca    1.7 Adult InseminatedFemale Spermatheca    4.6 Adult Ovary no informative data Adult Testis    1.4 Adult Male Accessory Gland    3.6 Adult Carcass    6.9 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary no informative data Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    3.2   NA  Eye    3.15   NA  Brain    4.4   3.375  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    2.1   NA  Crop    4.1   1.6  Midgut    2   1  Hindgut    1.2   2.8  Malpighian Tubules    3.3   2.1  Fat Body    6.2   2.7  Salivary Gland    4.9   NA  Heart    2.6   3.275  Trachea    NA   NA  VirginFemale Spermatheca    1.7   NA  InseminatedFemale Spermatheca    4.6   NA  Ovary    no informative data   NA  Testis    1.4   NA  Male Accessory Gland    3.6   2.2  Carcass    6.9 modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010, The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_31
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004053 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1046-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for zen Stages(s) 4-6 Stages(s) 7-8
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | embryonic stage zen2 zen3 zen4 zen5 lethal | embryonic stage | heat sensitive zen1 lethal | heat sensitive zen1 lethal | recessive zen7 zen436 zen714 viable zen1 viable, with Scer\GAL4pnr-MD237 zenGD4145 Other Phenotypes Allele wild-type zen+t4.5 Phenotype manifest in Allele cuticle zen7 denticle belt zen7 ectoderm | dorsal zen7 embryonic head zen1 zen5 embryonic head epidermis | dorsal zen4 embryonic optic lobe primordium zen4 extended germ band embryo zen7 optic lobe zen1 zen2 zen4 zen5 zen7 presumptive embryonic/larval central nervous system zen7 retina | ventral, with Scer\GAL4ey.PH zenScer\UAS.cAa
Classical Alleles ( 10 )
For All Classical Alleles Show
Allele of zen Class Mutagen Stocks Known lesion zen7 amorphic allele - genetic evidence, loss of function allele ethyl methanesulfonate 4 Yes zen4 loss of function allele ethyl methanesulfonate 2 -- zen1 hypomorphic allele - genetic evidence ethyl methanesulfonate 1 -- zen2 loss of function allele ethyl methanesulfonate 1 -- zen3 loss of function allele ethyl methanesulfonate 1 -- zen5 loss of function allele, hypomorphic allele - genetic evidence ethyl methanesulfonate 1 -- zenMAS1 loss of function allele ethyl methanesulfonate 1 -- zen436 ethyl methanesulfonate 0 -- zen6 loss of function allele ethyl methanesulfonate 0 -- zen714 ethyl methanesulfonate 0 --
Alleles Carried on Transgenic Constructs ( 20 )
For All Alleles Carried on Transgenic Constructs Show
Allele of zen Class Mutagen Stocks Known lesion zenhsp70.PR in vitro construct - regulatory fusion 2 Yes zenGD4145 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes zenHMS01109 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes zenJF02127 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes zenKK113335 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes zen+t4.5 in vitro construct - genomic fragment 0 Yes zenAct5C.PB in vitro construct - regulatory fusion 0 Yes zenAct5C.PH in vitro construct - regulatory fusion 0 Yes zenbcd.3UTR.Hsp83.T:Hsim\VP16 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes zenbcd.3UTR.Hsp83 in vitro construct - regulatory fusion 0 Yes zenbcdUTR.hs in vitro construct - regulatory fusion 0 Yes zenDel.Scer\UAS in vitro construct - regulatory fusion 0 Yes zenScer\UAS.cAa in vitro construct - regulatory fusion 0 Yes zenScer\UAS.cKa in vitro construct - regulatory fusion 0 Yes zenScer\UAS.cXa in vitro construct - regulatory fusion 0 Yes zenST.T:Scer\GAL4 in vitro construct - coding region fusion 0 Yes zentld.PR in vitro construct - regulatory fusion 0 Yes zentld.T:Hsim\VP16 in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes zenΔ1.Act5C in vitro construct - deletion in vitro construct - regulatory fusion 0 Yes zenΔ2.Act5C in vitro construct - deletion in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3R)ama (Fremion et al., 2000) Df(3R)Antp-X1 (Hazelrigg and Kaufman, 1983) Df(3R)Antp-X2 (Hazelrigg and Kaufman, 1983) Df(3R)BSC422 (Christensen et al., 2008.4.15) Df(3R)BSC467 (Christensen et al., 2008.4.15) Df(3R)D830 (Fremion et al., 2000) Df(3R)Dfd13 (Hazelrigg and Kaufman, 1983) Df(3R)Dfdrv1 (Gonzalez-Reyes and Morata, 1991) Df(3R)G63 (Muller et al., 1999) Df(3R)LIN (Jurgens and Weigel, 1988) Df(3R)MAP11 (Merrill et al., 1989) Df(3R)MAP117 (Kaufman et al., 1990) Df(3R)SCB-XL2 (Kaufman, 1994.10.5) Df(3R)Scr (Nicholls and Gelbart, 1998, Wakimoto et al., 1984, Merrill et al., 1989, Kaufman et al., 1990, Lewis et al., 1980) Df(3R)Scx2 (Hazelrigg and Kaufman, 1983, Wakimoto et al., 1984, Kaufman et al., 1990, Long et al., 1996)
Not disrupted in	Df(3R)Antp17 (Wakimoto et al., 1984, Kaufman et al., 1990, Lewis et al., 1980) Df(3R)Hu (Hazelrigg and Kaufman, 1983) Df(3R)MAP2 (Merrill et al., 1989) Df(3R)MAP8 (Kaufman et al., 1990) Df(3R)Scx3 (Hazelrigg and Kaufman, 1983) Df(3R)Scx4 (Hazelrigg and Kaufman, 1983, Kaufman et al., 1990) Dp(3;3)Antp73b-rv8 (Hazelrigg and Kaufman, 1983) In(3R)Antprv9 (Hazelrigg and Kaufman, 1983) In(3R)ScrWrv5 (Hazelrigg and Kaufman, 1983) T(2;3)Antprv5 (Hazelrigg and Kaufman, 1983) T(2;3)Antprv6 (Hazelrigg and Kaufman, 1983) T(2;3)Antprv7 (Hazelrigg and Kaufman, 1983) T(2;3)ScrWrv1 (Hazelrigg and Kaufman, 1983) T(2;3)ScrWrv6 (Hazelrigg and Kaufman, 1983) Tp(3;3)Dfdrv1 (Hazelrigg and Kaufman, 1983) Tp(3;3)Dfdrv3 (Hazelrigg and Kaufman, 1983)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{0.2zen-lacZ} No P{0.3} No P{0.04zen-lacZ} No P{0.7} No P{1.0zen-lacZ} No P{1.3} No P{1.4} No P{1.6zen-lacZ} No P{2x110bpVRE.mAT1} No P{2x110bpVRE.mAT2.I} No P{2x110bpVRE.mAT12} No P{2x110bpVRE} No P{2x180bpVRE} No P{2xVRE200.5.MSE.eve/lacZ} No P{2xVRE200.10.MSE.eve/lacZ} No P{2xVRE200.mAT1.mAT3.MSE.eve/lacZ} No P{2xVRE200.mAT1.MSE.eve/lacZ} No P{2xVRE200.mAT2.MSE.eve/lacZ} No P{2xVRE200.MSE.eve/lacZ} No P{4x50bpVRE} No P{4x70bpVRE} No P{7x37bpVRE} No P{180bpVRE.mAT} No P{180bpVRE.mGC} No P{180bpVRE} No P{350bpVRE} No P{430bpVRE} No P{lacZzen/eve.600bpVRE} No P{lacZzen/eve.mVR/MSE} No P{lacZzen/eve.tVR/MSE} No P{lacZzen/twi-VR/2PE} No P{lacZzen.3dl.hs} No P{lacZzen.3dl} No P{MSE.eve/lacZ.rVRE} No P{MSE.eve/lacZ.VRE} No P{St2.VRE600.St3.eve/lacZ} No P{St3.VRE600.St2.eve/lacZ} No P{VR600-su(Hw)-St.2} No P{zen:eve-lacZ.mutII} No P{zen:eve-lacZ.mutIII} No P{zen:eve-lacZ.mutIV} No P{zen-BR-eve-lacZ.VS2} No P{zen-BR-eve-lacZ.VSS2} No P{zen-eve-lacZ.V2} No P{zen-hb-lacZ} No P{zen-Kr-hsp70-lacZ} No P{zen-lacZ.666} No P{zen-lacZ.mut.B1.B2.B3.B5} No P{zen-lacZ.mut.B1.B2} No P{zen-lacZ.mut.M3.M4} No P{zen-lacZ.Δ161-131} No P{zen-lacZ.Δ217-178} No P{zen-lacZ.Δ292-43} No P{zen-lacZ.Δ476-350} No P{ΔAcc} No P{ΔNru} No P{ΔRsa} No P{ΔXmn} No UAS construct P{GD4145} NA P{KK113335} NA P{TRiP.HMS01109} NA P{TRiP.JF02127} NA P{UAS-zen.A} NA P{UAS-zen.Del} NA P{UAS-zen.K} NA P{UAS-zen.X} NA heat-shock construct P{hsp83-zen-bcdUTR} NA P{hs-zen} NA P{zen-bcd} NA P{zen-VP16-bcd} NA characterization construct P{tld-zen} NA P{tld-zenVP16} NA P{zen+4.5} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 10 unique terms )
Terms Based on Experimental Evidence ( 5 terms )
Molecular Function
CV term Evidence References
sequence-specific distal enhancer binding RNA polymerase II transcription factor activity inferred from direct assay (Rusch and Levine, 1997) sequence-specific DNA binding inferred from direct assay (Lin et al., 2006)
Biological Process
CV term Evidence References
compound eye development inferred from mutant phenotype (Anderson et al., 2006) negative regulation of gene expression inferred from direct assay (Anderson et al., 2006) positive regulation of transcription from RNA polymerase II promoter inferred from direct assay (Rusch and Levine, 1997)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
sequence-specific DNA binding transcription factor activity inferred from sequence or structural similarity with UniProtKB:Q08624 (FlyBase, 1992-)
Biological Process
CV term Evidence References
amnioserosa formation traceable author statement (Raftery and Sutherland, 2003) dorsal/ventral axis specification traceable author statement (Lall and Patel, 2001) dorsal/ventral pattern formation, imaginal disc non-traceable author statement (Swiss-Prot Project Members, 1988.11.1)
Cellular Component
CV term Evidence References
nucleus inferred from sequence or structural similarity with UniProtKB:Q08624 (FlyBase, 1992-) non-traceable author statement (Swiss-Prot Project Members, 1988.11.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions zen allele Gene References zen1 Mad (Hudson et al., 1998) Med (Hudson et al., 1998) sog (Decotto and Ferguson, 2001) unspecified brm (Armstrong et al., 2005) dpp (Nicholls and Gelbart, 1998) tor (Strecker et al., 1992)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 66026 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0004053 DroID - A comprehensive database of gene and protein interactions. • FBgn0004053 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40828
Orthologs
Genome-wide drosophilid orthologs	Dana\GF17795 Dere\GG10235 Dgri\GH19481 Dmoj\GI24719 Dper\GL22044 Dpse\zen Dsec\GM10527 Dsim\GD19522 Dvir\zen Dwil\GK10829 Dyak\GE25830
Curated drosophilid orthologs	Dbuz\zen   Dpse\zen   Dsub\zen   Dvir\zen
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • BGIBMGA007917-PA Bombyx mori (silk worm) CE42831 Caenorhabditis elegans (worm) CPIJ001003 Culex pipens (mosquito) ENSDARP00000023072 Danio rerio (zebra fish) ENSGACP00000007434 Gymnopilus aculeatus (mushroom) 86957 Hypsipyla robusta (cedar shoot borer) LOC_Os02g35770.1 Oryza sativa (asian rice) 120051 Physcomitrella patens (moss) ENSPPYP00000009098 Pongo pygmaeus (orangutan) 4813232 Sorghum bicolor (sorghum) 49524 Trichoplax adhaerens (metazoa) ENSXETP00000023041 Xenopus tropicalis (frog) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • FBgn0242880 FBgn0212840 FBgn0013150 FBgn0191017 FBgn0165473 FBgn0243538 FBgn0159636 FBgn0147441 FBgn0137033 FBgn0126946 FBgn0102545 FBgn0094813
Stocks & Reagents
Stocks Listed in FlyBase ( 17 )
Bloomington	30851 w*; P{hs-zen}1 30850 y1 w*; P{hs-zen}12 2262 zen2 pp/TM3, Sb1 2263 zen3 pp/TM3, Sb1 2264 zen4 pp/TM3, Sb1 3232 zen5 pp/TM3, Sb1 26229 y1 v1; P{TRiP.JF02127}attP2 2261 zen1 pp/TM3, Sb1 Ser1 2042 zen7 ftz11 e1/TM3, Sb1
Kyoto	106760 zen4 pp/TM3, Sb1
VDRC	v102915 P{KK113335}VIE-260B v12649 w1118; P{GD4145}v12649/TM3
	More stocks available...
Genomic Clones ( 1 )
	BACR19D23 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 9 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones	DPiM_RT01114 RT01114
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones	RP004131093 RP004183898 RP004183931 RP004201818 RP004261523 RP004364634 RP004419957
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0004053 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40828
Antibody Information
	polyclonal (Rushlow et al., 1987)
Other Information
Discoverer
Etymology
	The name for the locus derives from the characteristic 'wrinkled' appearance of the germ band seen in the SEM at the time of normal germ-band retraction.
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: zen CG1046 (Zhao, 1999.11)
Source for database merge of
Additional comments
Other Comments
	The zen product negatively regulates dac expression. (Anderson et al., 2006) dl can activate transcription from zen and twi promoters, and additional Dsp1 inhibits the zen activation and increases the twi activation. (Brickman et al., 1999) zen directly activates the amnioserosa-specific expression of a downstream target gene, Ance. zen is an essential, but not sole mediator of the dpp pathway. (Rusch and Levine, 1997) zen ventral repression element (VRE) activity has been studied. (Cai et al., 1996) Binding sites for the grh transcription factor contribute to the ventral repression of zen. (Huang et al., 1995) A putative dpp/zen target gene, Ance, is a homologue of the angiotensin converting enzyme is expressed in the presumptive amnioserosa. (Rusch et al., 1995) DNApol-α180 and mus209 are negatively regulated by zen protein. This repression is mediated by the DRE (DNA replication-related element) sites in the DNApol-α180 and mus209 promoters. The amount of Dref is reduced in transfected Kc cells expressing zen, suggesting that zen represses expression of DNA replication-related genes by reducing the amount of Dref. (Hirose et al., 1994) A minimal 110bp Ventral Repression Element silencer in the zen promoter contains two dl binding sites as well as binding sites for additional nuclear factors present in early embryos. Mutations in the latter convert the minimal VRE into an enhancer, mediating transcriptional activation in ventral regions in response to dl. (Jiang et al., 1993) dl binding sites from the zen promoter can mediate transcriptional activation of a heterologous promoter, but not repression. T-rich sequences close to the dl binding sites in the silencer region of the zen promoter are conserved between D.melanogaster, D.virilis and D.pseudoobscura.pseudoobscura. (Kirov et al., 1993) The homologs of Antp, ftz, Scr, Dfd, Ama, bcd, zen, pb and lab, but not zen2 are all present in D.pseudoobscura.pseudoobscura, in the same linear order and similarly spaced along the chromosome as in D.melanogaster. (Randazzo et al., 1993) Comparative analysis of the homeobox sequences reveals the subdivision of the Antp-type homeobox genes into three classes early in metazoan evolution, one includes Abd-B, the second includes abd-A, Ubx, Antp, Scr, Dfd and ftz, and the third includes zen, zen2, pb and lab. (Schubert et al., 1993) zen alleles display relative phenotypic strengths, this may be correlated to the progressive loss of dorsal pattern elements in the ventralised mutants. (Arora and Nusslein-Volhard, 1992) zen expression assayed in embryos from females expressing dl-lacZ fusion proteins compared to wild type dl. Consistant with degree of dorsalization, domain of zen expression is expanded laterally. (Govind et al., 1992) dl binding site domain exchange experiments, using Ecol\lacZ reporter gene constructs, between the zen and twi promoters demonstrate that dl is intrinsically an activator and that repression requires additional factors present in the distal region of the zen promoter, the VR. (Jiang et al., 1992) zen gene product is required for proper development of the amnioserosa. (Panzer et al., 1992) The zygotically acting DV genes repress ac expression within specific DV domains. (Skeath et al., 1992) dl is a sequence specific DNA binding protein that may mediate long range repression by interacting with the distal regions of the zen promoter. (Ip et al., 1991) dl-binding sites present in the twi promoter possess a lower affinity to those present in the zen promoter. (Jiang et al., 1991) Mutations in zygotic dorsal class gene zen do not interact with RpII140wimp. (Parkhurst and Ish-Horowicz, 1991) zen has altered pattern of expression in ventralized and lateralized embryos. In dorsalized embryos zen expression refines at stage 5. Polar expression of zen requires genes of the terminal group. zen is required for the normal ontogeny of the zen pattern and fating of the amnioserosa. (Ray et al., 1991) zen represses transcription from the mus209 promoter of mus209-Ecol\CAT reporter constructs. (Yamaguchi et al., 1991) Mutations result in loss of several dorsally derived embryonic structures, disruption of germ band extension and disruption of head involution. Optic lobe and the amnioserosa are most sensitive to loss of zen+ activity. Analysis of a temperature sensitive allele demonstrates the time of zen function is from 2--4 hours of embryogenesis. (Kaufman et al., 1990) Involved in the regulatory hierarchy responsible for the asymmetric distribution and function of zygotic regulatory gene products along the DV axis of early embryos. (Rushlow and Levine, 1990) In vitro DNA footprinting analysis shows that eve and zen can bind to sites in the mus209 5' flanking region. (Yamaguchi et al., 1990) The zen promoter shows a two-tier organization: distal sequences mediate its initial response to maternal factors, whereas proximal sequences are responsible for the refinement of the pattern in older embryos. The distal element has the property of a silencer (or anti-enhancer). The proximal element may interact with factors that may be modulated by a cell-cell communication pathway. (Doyle et al., 1989) A transient expression assay has been employed to investigate the potential of homeobox genes to function as transcriptional activators. (Han et al., 1989) The DNA binding activities of the en, eve, prd and zen proteins have been compared. (Hoey and Levine, 1988) P element mediated transformation experiments demonstrate that zen alone can provide zen+ gene function. This suggests that the neighbouring zen2 gene may be dispensable. (Rushlow et al., 1987) Null mutations result in embryonic lethality and the loss of several dorsally derived embryonic structures, including the amnioserosa, optic lobe and dorsal ridge. These animals also fail to fully extend their germ bands and go through the process of head involution. Hypomorphic mutations result in the absence of dorsal structures but do undergo normal gastrulation movements. A temperature-sensitive allele has been used to define the time of zen+ action between 2 and 4 hours of embryogenesis, just prior to and overlapping the earliest observable morphogenic defects. X-ray induced somatic clones have further shown that zen+ function is unnecessary for postembryonic development. The RNA product of zen is first detected at about 2 hours of development during the eleventh to twelfth cell cycle of the syncytial blastoderm. At this early stage the RNA is found on the dorsal surface of the embryo extending around the anterior and posterior poles. As cellularization proceeds and the early events of gastrulation begin, the RNA becomes restricted to a mid-dorsal stripe of cells. These cells have been fate mapped and give rise to the amnioserosa and the lobes in the dorsal posterior of the embryonic head, i.e., the structures absent in zen- animals. The time of appearance of zen RNA also correlates nicely with the temperature-sensitive-period data obtained using the conditional allele. Antisera to the zen protein product has been used to follow its accumulation pattern and this analysis agrees with and expands the in situ results. The protein is located in the nuclei of cells expressing the gene and at cellular blastoderm is found in a mid-dorsal stripe seven cells wide and seventy cells in length. During gastrulation these cells eventually give rise to the amnioserosa, the optic lobe and dorsal ridge; these structures continue to show zen protein accumulation until the end of germ-band extension at about 4 to 6 hours of development. This end point also correlates well with the end of the temperature-sensitive period of the conditional allele. The spatial pattern of zen expression has been shown to be dependent on the products of several of the maternally expressed genes which specify the anterior-posterior and dorsal-ventral polarity of the embryo, and zen would appear to lie near the end of the axis-determining pathway.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057445 RefSeq (Proteins) • NP_476793 DDBJ / EMBL / GenBank • AAD19800 AAF54087 AC002512 ACL83477 AE001572 CAA48416 L18923 S78213 X68347 Entrez Gene - A searchable database of RefSeq genes. • 40828 UniProtKB/Swiss-Prot • P09089
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Homeobox, conserved site (IPR017970) Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) Homeobox, eukaryotic (IPR020479)
Linkouts
	BioGRID - A database of protein and genetic interactions • 66026 DPiM - DPiM, Drosophila Protein interaction Map • FBgn0004053 DroID - A comprehensive database of gene and protein interactions. • FBgn0004053 DRSC - Results from RNAi screens. • FBgn0004053 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0004053 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG1046-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0004053 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 40828 InParanoid A subset of ortholog calls from InParanoid. • BGIBMGA007917-PA Bombyx mori (silk worm) CE42831 Caenorhabditis elegans (worm) CPIJ001003 Culex pipens (mosquito) ENSDARP00000023072 Danio rerio (zebra fish) ENSGACP00000007434 Gymnopilus aculeatus (mushroom) 86957 Hypsipyla robusta (cedar shoot borer) LOC_Os02g35770.1 Oryza sativa (asian rice) 120051 Physcomitrella patens (moss) ENSPPYP00000009098 Pongo pygmaeus (orangutan) 4813232 Sorghum bicolor (sorghum) 49524 Trichoplax adhaerens (metazoa) ENSXETP00000023041 Xenopus tropicalis (frog) Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution • /torstoll/zerknlt1.htm InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 40828 modMine - Data generated by the modENCODE project. • FBgn0004053 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • FBgn0242880 FBgn0212840 FBgn0013150 FBgn0191017 FBgn0165473 FBgn0243538 FBgn0159636 FBgn0147441 FBgn0137033 FBgn0126946 FBgn0102545 FBgn0094813 REDfly - A database of transcriptional regulatory elements. • FBgn0004053
Synonyms & Secondary IDs ( 13 )
Reported As
Symbol Synonym	BG:DS00276.9   CG1046 (Perkins et al., 2009.3.31, Keleman et al., 2009.8.5, Brandt, 2006, Ni et al., 2010.12.1) l(3)84Ad   z1 (Kourakis et al., 1997, Rushlow and Levine, 1990, Rushlow et al., 1987, ) zen (ten Bosch et al., 2006, Pearson et al., 2005, Peel et al., 2005, Negre and Ruiz, 2007, Lin et al., 2006, Nien et al., 2007, Gunaydin et al., 2007, Kumar and Anderson, 2007, Scuderi et al., 2006, Chen et al., 2006, Hoskins et al., 2005, Zeitlinger et al., 2007, Friedrich, 2006, Stathopoulos and Levine, 2005, Ratnaparkhi et al., 2006, Aerts et al., 2007, Barker et al., 2005, Chen et al., 2000, Roy et al., 2007, Christensen et al., 2008.4.15, Christensen et al., 2008.4.15, Schmidt-Ott, 2005, Duboule, 2007, Ullah et al., 2007, Kwong et al., 2008, Riede, 2004, Astigarraga et al., 2007, Pope and Harris, 2008, Li et al., 2008, Miles et al., 2008, Liang et al., 2008, Casillas et al., 2006, Demuth and Wade, 2007, Brandt, 2006, Shirangi et al., 2006, Kazemi-Esfarjani and Benzer, 2002, Rafiqi, 2010.5.12, Negre et al., 2005, Salzer et al., 2010, Hueber et al., 2010, Bai et al., 2009, Gurunathan et al., 2004, Jia et al., 2002, Tipping et al., 2010, Harrison et al., 2010, Su et al., 2010, Beltran et al., 2007, Roy et al., 2011, Kazemian et al., 2010) Zen (De Renzis et al., 2007) zen1 (Finnerty and Martindale, 1998) ZEN VRE (Senger et al., 2004)
Name Synonym	zerknuellt (Friedrich, 2006) zerknullt (ten Bosch et al., 2006, Kumar and Anderson, 2007, Pilot et al., 2006, Anderson et al., 2006, Ratnaparkhi et al., 2006, Barker et al., 2005, Roy et al., 2007, Schmidt-Ott, 2005, Astigarraga et al., 2007, Pope and Harris, 2008, Miles et al., 2008, Wang et al., 2008, Casillas et al., 2006, Demuth and Wade, 2007, Shirangi et al., 2006, Negre et al., 2005, Bai et al., 2009) Zerknullt (Hueber et al., 2010) zerknullt 1 (Martin, 1999.1.14) zerknult (Kortschak et al., 2000, Li et al., 2008, Salzer et al., 2010)
Secondary FlyBase IDs
	FBgn0013967 FBgn0019915
References ( 326 )
Generate a list of	All references relating to this gene ( 326 )
List References by type	Research paper  ( 173 ) Supplementary material  ( 4 ) Review  ( 90 ) Personal communication to FlyBase  ( 11 ) Abstract  ( 34 ) FlyBase analysis  ( 2 ) DNA/RNA sequence record  ( 1 ) Curated genome annotation  ( 2 ) Protein sequence record  ( 1 ) Computer file  ( 1 ) Conference report  ( 4 ) Stock list  ( 1 ) Automatic genome annotation  ( 1 ) Book  ( 1 )
Recent research papers ( 7 )
	Roy et al., 2011, Mol. Genet. Genomics 285(2): 113--123 Lack of the Drosophila BEAF insulator proteins alters regulation of genes in the Antennapedia complex. [FBrf0212912] Harrison et al., 2010, Dev. Biol. 345(2): 248--255 Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes. [FBrf0211626] Hueber et al., 2010, PLoS ONE 5(5): e10820 Improving Hox protein classification across the major model organisms. [FBrf0210952] Kazemian et al., 2010, PLoS Biol. 8(8): Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. [FBrf0211688] Salzer et al., 2010, Genetics 184(1): 185--197 The retinal determination gene eyes absent is regulated by the EGF receptor pathway throughout development in Drosophila. [FBrf0209690] Su et al., 2010, PLoS Comput. Biol. 6(12): e1001020 Assessing Computational Methods of Cis-Regulatory Module Prediction. [FBrf0212482] Tipping et al., 2010, EMBO J. 29(19): 3222--3235 β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development. [FBrf0211995] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...