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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
Created / Updated	2003-12-01/2008-03-05
Genomic Location
Chromosome (arm)	3R	Recombination map	3-47.5
Cytogenetic map	84A5-84A5	Sequence location	3R:2,578,586..2,582,059 [-]
Map ( 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 zen (CG1046, FBgn0004053). It has the cytological map location 84A5. Its sequence location is 3R:2578586..2582059. Its molecular function is described as: sequence-specific DNA binding; specific RNA polymerase II transcription factor activity; specific transcriptional repressor activity; transcription factor activity. It is involved in the biological processes: dorsal/ventral pattern formation, imaginal disc; dorsal/ventral axis specification; amnioserosa formation; compound eye development; regulation of transcription, DNA-dependent. 25 alleles are reported. The phenotypes of these alleles are annotated with: embryonic head; optic lobe; embryonic head epidermis; embryonic optic lobe primordium; extended germ band embryo; cuticle; denticle belt; embryonic central nervous system; retina. It has 2 annotated transcripts and 2 annotated polypeptides.
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.
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
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\zen for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) zen-RA FBtr0081670  NM_057445   1272   353 zen-RB FBtr0290294     1236   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 (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein zen-PA   FBpp0081170   39.3   353   9.58     NP_476793   AAF54087 zen-PB   FBpp0288733   39.3   353   9.58
Additional Polypeptide Data & Comments
Reported size (kD)	353 (aa); 39 (kD predicted) (Rushlow et al., 1987)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0004053
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Helix-turn-helix motif, lambda-like repressor (IPR000047) Homeobox (IPR001356) Homeodomain-like (IPR009057) Homeodomain-related (IPR012287) TRANSFAC - Eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles • R01723 R02852 R02853 R02854 T00917
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AC002512   AE001572 AAD19800   AE003674 AAF54087   AI388613   BG637717   BG638487   BT021332   BT028847   CO186396   CO289714   CO290079   CO293384   CO303499   EC058772   EC062997   EC065675   EC080133   EC083912   EC086584   EC229305   EC230739   EC245288   EL877622   EL877741   EL877868   EL877992   L18923   LD01105   LD27003   S78213   X68347 CAA48416
UniProtKB/Swiss-Prot	P09089
UniProtKB/TrEMBL
Maps to	DS00276 (FlyBase, 1992-)
Does NOT map to
Identified with	D1411 (BDGP Project Members, 1994-1999)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References aberration junction Df(3R)LIN.bk1 3R:2,578,121..2,579,258 comment=Aberration breakpoint localized to a restriction fragment; position of restriction fragment on reference sequence inferred by FlyBase curator. evidence=experimental linked_to=BamHI-BamHI_rfrag (Rushlow et al., 1987) protein binding site zen-protein_bind-6 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, Jiang et al., 1993) protein binding site zen-protein_bind-5 3R:2,581,202..2,581,214 comment=GC2 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004, Jiang et al., 1993) protein binding site zen-protein_bind-8 3R:2,581,253..2,581,265 comment=GC1 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004, Jiang et al., 1993) protein binding site zen-protein_bind-7 3R:2,581,238..2,581,250 comment=AT1 evidence=experimental (Jiang et al., 1993, Bergman et al., 2004) protein binding site zen-protein_bind-4 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 zen-protein_bind-3 3R:2,581,170..2,581,180 comment=DL_binding_site_ZD2; one of several fragments within the VRE bound by dl protein evidence=experimental bound_moiety=dl-P* bound_moiety=dl-XP (Jiang et al., 1993, Ip et al., 1991, Bergman et al., 2004) protein binding site zen-protein_bind-2 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 zen-protein_bind-1 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 zen-protein_bind-10 3R:2,580,333..2,580,344 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-11 3R:2,580,283..2,580,295 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001, Jiang et al., 1993) protein binding site zen-protein_bind-12 3R:2,579,958..2,579,970 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-13 3R:2,580,553..2,580,568 bound_moiety=brk-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-14 3R:2,580,148..2,580,167 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-15 3R:2,580,464..2,580,492 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-16 3R:2,580,045..2,580,072 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-17 3R:2,580,147..2,580,160 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-18 3R:2,580,199..2,580,218 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-19 3R:2,580,310..2,580,324 bound_moiety=Mad-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-20 3R:2,580,196..2,580,208 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-21 3R:2,580,051..2,580,066 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) protein binding site zen-protein_bind-22 3R:2,579,983..2,579,995 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-9 3R:2,580,282..2,580,294 bound_moiety=brk-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001, Jiang et al., 1993) protein binding site zen-protein_bind-23 3R:2,581,266..2,581,278 bound_moiety=Mad-XP evidence=experimental (Bergman et al., 2004, Rushlow et al., 2001) protein binding site zen-protein_bind-24 3R:2,581,252..2,581,271 bound_moiety=grh-XP evidence=experimental (Bergman et al., 2004, Huang et al., 1995) protein binding site zen-protein_bind-25 3R:2,581,266..2,581,277 bound_moiety=brk-XP evidence=experimental (Rushlow et al., 2001, Bergman et al., 2004) regulatory region zen-reg_element-2 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 zen-reg_element-3 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 zen-reg_element-4 3R:2,581,264..2,581,270 comment=DRE evidence=experimental (Huang et al., 1995) regulatory region zen-reg_element-13 3R:2,580,209..2,580,591 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 linked_to=EcoRI-AccI_rfrag (Doyle et al., 1989) rescue fragment zen[+t4.5] 3R:2,577,103..2,581,527 comment=Position of restriction fragment on reference sequence inferred by FlyBase curator. evidence=experimental linked_to=XbaI-SstI_rfrag (Rushlow et al., 1987)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 8509
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  embryonic stage | extended germ band stage  dorsal ectoderm | restricted (Rushlow et al., 1987)  embryonic stage | extended germ band stage  pole cell | restricted (Rushlow et al., 1987)  embryonic stage | stage 3   (Doyle et al., 1986)  embryonic stage | embryonic cycle 14   (Rushlow et al., 1987)  embryonic stage   (Rushlow et al., 1987)  embryonic stage | stage 7-10  dorsal ectoderm | restricted (Doyle et al., 1986)  embryonic stage | stage 4-6   (Doyle et al., 1986)  dorsal ectoderm   (Doyle et al., 1986)  embryonic stage | stage 6-7  NOT hindgut anlage (Podos et al., 2001)  embryonic stage | gastrulation   (Rushlow et al., 1987)  embryonic stage | stage 4  dorsal ectoderm (Doyle et al., 1986)  embryonic stage | stage 6-7  amnioserosa (Podos et al., 2001)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference  embryonic stage | stage 3-11  dorsal ectoderm | restricted (Rushlow et al., 1987)
Marker for
Subcellular Localization
CV Term
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 • FBgn0004053 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0004053 FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for zen Stage(s) 1-3 Stage(s) 4-6 Stage(s) 7-8 Stage(s) 9-10 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable zen1 lethal | recessive zen436 zen714 zen7 lethal | conditional - heat sensitive zen1 lethal | embryonic stage zen2 zen3 zen4 zen5 lethal | embryonic stage | conditional - heat sensitive zen1 Other Phenotypes Allele wild-type zen+t4.5 Phenotype manifest in Allele embryonic head zen1 zen5 optic lobe zen1 zen2 zen4 zen5 zen7 embryonic head epidermis | dorsal zen4 embryonic optic lobe primordium zen4 extended germ band embryo zen7 cuticle zen7 denticle belt zen7 embryonic central nervous system zen7 ectoderm & embryo | dorsal 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 zen1 hypomorph ethyl methanesulfonate 1 -- zen2 loss of function ethyl methanesulfonate 1 -- zen3 loss of function ethyl methanesulfonate 1 -- zen436 ethyl methanesulfonate 0 -- zen4 loss of function ethyl methanesulfonate 2 -- zen5 loss of function, hypomorph ethyl methanesulfonate 1 -- zen6 loss of function ethyl methanesulfonate 0 -- zen714 ethyl methanesulfonate 0 -- zen7 amorph, loss of function ethyl methanesulfonate 4 Yes zenMAS1 loss of function ethyl methanesulfonate 1 --
Alleles Carried on Transgenic Constructs ( 15 )
For All Alleles Carried on Transgenic Constructs Show
Allele of zen Class Mutagen Stocks Known lesion 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 zenDel.Scer\UAS in vitro construct | regulatory fusion 0 Yes zenGD4145 in vitro construct | RNAi in vitro construct | regulatory fusion 1 Yes zenST.T:Scer\GAL4 in vitro construct | coding region fusion 0 Yes zenScer\UAS.cAa in vitro construct | regulatory fusion 0 Yes zenScer\UAS.cXa 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 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
Useful deficiency	Df(3R)BD5   Df(3R)MAP117
Useful duplication	Dp(3;Y)77ab
Disrupted in	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) Df(3R)ama (Fremion et al., 2000)
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{0.04zen-lacZ} No P{0.2zen-lacZ} No P{0.3} No P{0.7} Yes P{1.0zen-lacZ} Yes P{1.3} Yes P{1.4} Yes P{1.6zen-lacZ} Yes P{180bpVRE.mAT} No P{180bpVRE.mGC} No P{180bpVRE} No P{2x110bpVRE.mAT12} No P{2x110bpVRE.mAT1} No P{2x110bpVRE.mAT2.I} No P{2x110bpVRE} No P{2x180bpVRE} No P{2xVRE200.10.MSE.eve/lacZ} No P{2xVRE200.5.MSE.eve/lacZ} No P{2xVRE200.MSE.eve/lacZ} No P{2xVRE200.mAT1.MSE.eve/lacZ} No P{2xVRE200.mAT1.mAT3.MSE.eve/lacZ} No P{2xVRE200.mAT2.MSE.eve/lacZ} No P{350bpVRE} No P{430bpVRE} No P{4x50bpVRE} No P{4x70bpVRE} No P{7x37bpVRE} No P{MSE.eve/lacZ.VRE} No P{MSE.eve/lacZ.rVRE} No P{St2.VRE600.St3.eve/lacZ} No P{St3.VRE600.St2.eve/lacZ} No P{VR600-su(Hw)-St.2} No P{lacZzen.3dl.hs} No P{lacZzen.3dl} No P{lacZzen/eve.600bpVRE} Yes P{lacZzen/eve.mVR/MSE} No P{lacZzen/eve.tVR/MSE} No P{lacZzen/twi-VR/2PE} No P{zen-BR-eve-lacZ.VS2} No P{zen-BR-eve-lacZ.VSS2} No P{zen-Kr-hsp70-lacZ} No P{zen-eve-lacZ.V2} No P{zen-hb-lacZ} No