WormBase Model:Construct
From WormBaseWiki
back to WormBase_Models
Contents
Proposed model changes
Purpose: the technology of engineering mutations and gene replacement has been developed in C. elegans. With these new research tools, capture and display of the molecular information of these alleles needs to be updated. We propose a new class, Construct, to capture the specifics of the DNA tool used to perform the replacement or engineering, while the Variation model gets updated to record the engineering event itself and its impact on the genome. As a side benefit to the creation of the Construct model, we can use this new class to also capture the genomic arrays used create transgenes.
Example data
LP132 nmy-2(cp7[nmy-2::gfp + LoxP unc-119(+) LoxP]) I; unc-119(ed3) I
Variation
Proposed additions
?Variation Variation_type Engineered_allele Variation_summary //to house final engineered construct Derived_from ?Construct XREF Variation Method Homologous_recombination NHEJ MosSci Cas9 Crispr Expr_pattern ?Expr_pattern XREF Variation #Evidence
notes on variation model changes
see discussion tab
Construct (new)
Class itself is new
?Construct Name UNIQUE ?Text Summary ?Text Sequence feature ?Feature XREF Construct //hard coded list Gene ?Gene Gene_site_targeted ?SO_term Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. Other_reporter ?Text //to add reporters, tags that aren’t included in model Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. Type_of_construct Chimera Domain_swap Engineered mutation Fusion Complex_fusion // complex changes (e.g. GFP fusion plus point mutations) Transcriptional_fusion Translational_fusion N-terminal_translational_fusion C-terminal_translational_fusion Internal_coding_fusion Selection_marker ?Text //for unc-119(+), lin-15(+), drug selection Construction_summary ?Text // Clone ?Clone XREF Construct Used_for Transgene_construction ?Transgene XREF Construct Variation ?Variation XREF Engineered_allele Reference ?Paper XREF Construct Person ?Person XREF Construct Laboratory ?Laboratory #Lab_Location Remark ?Text #Evidence
notes on construct model
see discussion tab
Clone
?Clone Evidence #Evidence Remark General_remark ?Text Y_remark ?Text PCR_remark ?Text Position Map ?Map XREF Clone #Map_position Pmap UNIQUE ?Contig XREF Clone UNIQUE Int UNIQUE Int Clone_left_end ?Sequence Clone_right_end ?Sequence Pos_neg_data ?Pos_neg_data Positive Positive_gene ?Gene XREF Positive_clone Positive_variation ?Variation XREF Positive_clone ?Author Inside_rearr ?Rearrangement XREF Clone_inside ?Author Hybridizes_to ?Clone XREF Positive_probe ?Grid Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid Positive_probe ?Clone XREF Hybridizes_to ?Grid Pos_probe_weak ?Clone XREF Hybridizes_weak ?Grid Negative Negative_gene ?Gene XREF Negative_clone Negative_locus ?Locus XREF Negative_clone ?Author Outside_rearr ?Rearrangement XREF Clone_outside ?Author Negative_probe ?Clone XREF Does_not_hybridize_to ?Grid Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid In_strain ?Strain XREF Clone Species UNIQUE ?Species Sequence ?Sequence XREF Clone PCR_product ?PCR_product XREF Clone Length Seq_length UNIQUE Int Gel_length UNIQUE Float Location ?Laboratory #Lab_Location URL Text Gridded ?Grid Grid_data ?Grid_data FingerPrint Gel_Number UNIQUE Int Approximate_Match_to UNIQUE ?Clone XREF Canonical_for Exact_Match_to UNIQUE ?Clone XREF Canonical_for Funny_Match_to UNIQUE ?Clone XREF Canonical_for Canonical_for ?Clone UNIQUE Int UNIQUE Int Bands UNIQUE Int UNIQUE Int Gel ?Motif #Lane Contig9 Chromosome UNIQUE ?Map Vaxmap UNIQUE Float In_situ UNIQUE Int UNIQUE Int Cosmid_grid Canon_for_cosmid Flag UNIQUE Int Autopos Expression_construct Pattern ?Text Reference ?Paper XREF Clone cDNA_group Contains ?Clone XREF Contains Text Contained_in ?Clone XREF Contained_in Best_match UNIQUE ?Text Expr_pattern ?Expr_pattern XREF Clone Sequence_status Shotgun UNIQUE DateType Finished UNIQUE DateType Accession_number UNIQUE ?Text DB_info Database ?Database ?Database_field ?Accession_number XREF Clone Type UNIQUE Cosmid Fosmid YAC cDNA Plasmid Other Text Transgene ?Transgene XREF Clone Derived_from ?Clone
Transgene
Proposed changes
?Transgene Construction //Strain_construction Construct ?Construct XREF Transgene_construction Fragment Text ?Text //Can this be replaced by Construct? Coinjection_marker ?Text //remove?, replaced by selection_marker in ?Construct Used_for Topic_marker ?Process XREF Transgene