Summary
[Wormbase] The ced-3 gene encodes a protease required for apoptosis.
Wormbase predicts one model.
AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at high level, 1.7 times the average gene in this release, in embryos [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 100%, L3 to adult 0%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 13 cDNA clones and 9 elements defined by RNA-seq, some from embryo (seen 4 times).
The gene contains 7 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL1. There are 4 validated alternative polyadenylation sites (see the diagram). Function: There are 181 articles specifically referring to this gene in PubMed. In addition we point below to 166 abstracts. This essential gene is associated to a phenotype (CEll Death abnormality, Sterile adult). Functionally, the gene has been proposed to participate in processes (proteolysis and peptidolysis, regulation of apoptosis). Proteins are expected to have molecular functions (cysteine-type endopeptidase activity, protein binding activity) and to localize in intracellular. This protein appears to interact with other proteins (CED-4, CED-9, CED-12, DCT-1, FEM-1, MAC-1). The gene interacts with 35 other genes (ABL-1, BEC-1, BMK-1, CAR-1, CDL-1, CED-1, CED-2, CED-5, CED-7, CED-8, CED-9, CED-11, CED-13, CES-1, CES-2, CPB-3, CPS-6, CRN-1, CRN-2, CRN-4, CUP-5, DRP-1, EGL-1, EGL-47, GLD-1, HAM-1, MEV-1, NUC-1, PMK-3, SEL-10, SEL-12, SET-21, TRA-1, URI-1, WAH-1).
The spliced mRNA putatively encodes a good protein, containing domains Caspase Recruitment, Peptidase C14, caspase catalytic [Pfam].
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12. Map on chromosome IV, links to other databases and other names Map: This essential gene ced-3 maps on chomosome IV at position +8.46 (interpolated). In AceView, it covers 5.86 kb, from 13204099 to 13198245 (WS190), on the reverse strand. Links to:WormBase, NextDB, RNAiDB. Other names: The gene is also known in Wormgenes/AceView by its positional name 4N964, in Wormbase by its cosmid.number name C48D1.2, in NextDB, the Nematode expression pattern database, as CEYK4316. Closest AceView homologs in other species ? The closest human genes, according to BlastP, are the AceView genes CASP3 (e=7 10-33), CASP7 (e=8 10-33), TMEM139andCASP2 (e=10-30), PLA2G12AandCASP6 (e=4 10-30). The closest mouse genes, according to BlastP, are the AceView genes Casp7 (e=10-33), Casp2 (e=2 10-30), Casp3 (e=2 10-30), Casp6 (e=2 10-28)
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .a.
or in GIF: .a
[wbg13.3p44] Programmed Cell Death in the C. elegans Germ Line
[wbg13.2p70] A Presynaptic Defect in unc-26 Mutants?
[wm95p79] HUMAN BETA AMYLOID EXPRESSION IN TRANSGENIC C. ELEGANS
[wm95p143] SCREENING FOR CELL DEATH GENES AS SUPPRESSORS OF lin-24 and lin-33 MUTATIONS
[wbg14.1p94] Baculovirus p35 protein is a substrate for and inhibitor of the C. elegans cell-death protease CED-3
[wm95p178] STRUCTURE-FUNCTION STUDIES OF THE CELL DEATH PROTEIN CED-3.
[wm95p188] A Monopoly of the Undertakers? Some ced Genes That Mediate Removal of Programmed Cell Death Corpses Also Influence Removal of Degenerative Death Corpses
[wm95p242] HAM-1 DISTRIBUTES DEVELOPMENTAL POTENTIAL DURING SEVERAL ASYMMETRIC CELL DIVISIONS
[wm97e218] A Genetic Screen For Downstream Effectors of ICE
[wm97e244] TOWARD UNDERSTANDING CELL-TYPE SPECIFIC CELL DEATH REGULATION
[wm97e315] MUTATIONS IN cdl-1 RESULT IN EXCESS CELL CORPSES AND DEFECTIVE ELONGATION DURING EMBRYOGENESIS.
[wm97e411] A genetic screen for genes that control programmed cell death in the germ line
[wm97e562] POSSIBLE INHIBITOR-OF-APOPTOSIS PROTEINS (IAPs) IN C. ELEGANS
[wm97e566] THE ced-8 AND ced-11 GENES AFFECT THE TIMING AND MORPHOLOGY OF PROGRAMMED CELL DEATHS
[wm97e574] A DEFICIENCY SCREEN FOR REGIONS OF THE GENOME INVOLVED IN PROGRAMMED CELL DEATH
[wbg15.4p42] mev-1 and rad-8 embryos undergo massive apoptosis under high oxygen
[wbg15.4p40] The Pristionchus Hox gene Ppa-lin-39 inhibits programmed cell death to specify the vulva equivalence group and is not required during vulval induction.
[mwwm98p41] mac-1 encodes an essential protein that interacts with CED-4
[mwwm98p67] GENETIC AND MOLECULAR CHARACTERIZATION OF CDL-1, WHOSE MUTATIONS CAUSE EXCESS CELL CORPSES AND DEFECTIVE ELONGATION DURING EMBRYOGENESIS
[ewm98pt28] egl-1 IS REQUIRED FOR PROGRAMMED CELL DEATH IN THE SOMA AND ENCODES A BH3-CONTAINING PROTEIN THAT INTERACTS WITH CED-9
[ecwm98p172] MORPHOLOGY AND TIMING OF PROGRAMMED CELL DEATHS
[ecwm98p167] A GENETIC SCREEN FOR DEFECTS IN THE SPECIFICATION OF PROGRAMMED CELL DEATH IN THE POSTDEIRID LINEAGE
[ecwm98p161] GENETIC AND MOLECULAR ANALYSIS OF THE EXECUTION OF PROGRAMMED CELL DEATH
[ecwm98p2] A GENETIC SCREEN FOR GENES THAT CONTROL PROGRAMMED CELL DEATH IN THE GERM LINE.
[ecwm98p94] CED-3 IS NOT ALONE: IDENTIFICATION OF TWO FURTHER CASPASE HOMOLOGS IN C. ELEGANS
[ecwm98p89] ced(n3194), A SUPPRESSOR OF ced-9(n1950), MAY REPRESENT A NEW NEGATIVE REGULATOR OF CELL DEATH
[ecwm98p83] FURTHER STUDIES OF PROGRAMMED CELL DEATH IN THE GERMLINE
[ecwm98p5] A C. elegans Model for Huntington's Disease and other CAG Trinucleotide Repeat Diseases.
[ecwm98p73] A POLY(ADP-RIBOSE) POLYMERASE FROM CAENORHABDITIS ELEGANS: CLONING AND CHARACTERIZATION.
[ecwm98p1] egl-1 IS REQUIRED FOR PROGRAMMED CELL DEATH AND ENCODES A BH3-CONTAINING PROTEIN
[ecwm98p67] FUNCTIONAL REGULATION OF CED-4 SUBCELLULAR LOCALIZATION IN C. ELEGANS BY CED-9 AND UPSTREAM CELL-DEATH ACTIVATORS
[ecwm98p69] A SCREEN FOR GENES INVOLVED IN THE REMOVAL OF NECROTIC DEATH CORPSES: FURTHER EVIDENCE FOR A MONOPOLY OF THE UNDERTAKERS
[wm99p795] The inhibitor-of-apoptosis (IAP)-like protein BIR-1 is required for cytokinesis
[ecwm2000p107] CED-9 and EGL-1 regulate the subcellular localization of CED-4
[ecwm2000p110] egs-1 and egs-2 are required for HSN death
[ecwm2000ab112] Genetic analysis of DNA damage induced germline apoptosis
[ecwm2000p153] A screen for genes that control programmed cell death in the germ line
[ecwm2000p184] A screen for mutants defective in the specification of the programmed cell deaths of the male-specific CEM neurons
[euwm2000ab60] Genetic analysis of polyglutamine-mediated cellular dysfunction in C. elegans
[euwm2000ab101] Programmed cell death in the ventral epidermis of Pristionchus pacificus
[euwm2000ab143] Regulation of programmed cell death in the Germ line of C. elegans Hermaphrodites
[jwm2000p35] Characterization of a deficiency mutant that produces abnormally large cell corpses in late embryogenesis.
[mwwm2000p66] ced-12 is required for phagocytosis and cell migration
[wcwm2000p40] Neurotoxin sensitivity of dopaminergic neurons in C. elegans: role of the dopamine transporter and cell death pathways
[wcwm2000p48] A screen for genes that control programmed cell death in the germ line
[wcwm2000p51] Biochemical, structural, and genetic analyses of the activation of programmed cell death
[wcwm2000p50] Identification of cell-specific regulators of programmed cell death in C. elegans.
[wm2001p360] RNA interference, a way to check for inhibitors involved in germline cell death in Caenorhabditis elegans
[wm2001p361] A screen for genes that control programmed cell death in the germ line
[wm2001p362] What factors regulate programmed cell death in the germ line of C. elegans?
[wm2001p521] The ty10 mutation results in an unfused anchor cell that degenerates or detaches in L4 stage hermahprodites
[wm2001p603] Caenorhabditis elegans as a Model Host for Human Bacterial Pathogens
[wm2001p622] Nuclear Lamina Characterization in C. elegans during Apoptosis
[wm2001p625] Identification and characterization of cps-4 and cps-5
[wm2001p626] TWO NEW CELL-DEATH GENES AND ENGULFMENT CONTRIBUTE TO CELL KILLING
[wm2001p630] Characterization of a deficiency mutant that produces abnormally large cell corpses in late embryogenesis.
[wm2001p740] Genes that Affect Asymmetric Cell Division and Cell Fate in the Nervous System
[wm2001p832] Mitochondrial Complex I and II Defects Result in Excessive Superoxide Anion and Apoptosis.
[wm2001p121] Analysis of the Sex-Specific Death of the Male-Specific CEM Neurons
[wm2001p122] The cfi-1 gene inhibits expression of CEM cell fate in other C. elegans neurons.
[wm2001p124] A Genetic Pathway Involved In Apoptotic DNA Degradation In Nematodes
[wm2001p127] A Novel Pharmacogenetic Model for Parkinson's
[wm2001p176] HOW HOX WORKS? eff-1 is the name, effector of cell fusion is the game
[wm2001p253] cgh-1 , a conserved germline predicted RNA helicase required for gametogenesis and oocyte survival in C. elegans
[wm2001p296] C. elegans MUTANTS IN THE muc-1 GENE PROVIDE A MODEL FOR THE HUMAN LYSOSOMAL STORAGE DISEASE MUCOLIPIDOSIS TYPE IV
[wm2001p297] Mutations in the C elegans pqe-1 gene enhance polyglutamine-mediated ASH neurodegeneration
[wm2001p351] IDENTIFICATION OF TWO GENES THAT CONTROL THE SURVIVAL OF THE MALE-SPECIFIC CEM NEURONS
[wm2001p352] sue-1 and sue-2 are required for HSN death
[wm2001p353] Identification of Genes that Specify the Deaths of the Hemaphrodite-Specific Neurons
[wm2001p356] pvl-5 prevents Pn.p cell death during C. elegans vulval development.
[wm2001p357] Inactivation of hus-1, a conserved checkpoint gene in Caenorhabditis elegans, results in impaired cell cycle arrest and apoptosis induced by genotoxic stress.
[wm2001p359] abl-1 Regulates C. elegans Germ-cell Apoptosis
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !
