WormBase Model:CDS
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Curator Comments/Description
Model
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//
// ?CDS class - To store all coding genes
//
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?CDS Evidence #Evidence
SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF CDS_child
Transposon UNIQUE ?Transposon XREF CDS_child
Structure Source_exons Int UNIQUE Int
DB_info Database ?Database ?Database_field UNIQUE ?Accession_number XREF CDS
Protein_id ?Sequence UNIQUE Text UNIQUE Int // DB_info tag added [011030 krb]
DB_remark ?Text #Evidence
Origin From_laboratory UNIQUE ?Laboratory
Species UNIQUE ?Species
Genetic_code UNIQUE ?Genetic_code // needed for one gene with selenocysteine!
Properties Coding CDS UNIQUE Int UNIQUE Int
CDS_predicted_by ?Method Float // score of method
Prediction_status UNIQUE Predicted // all CDSs must be one of these three things
Partially_confirmed
Confirmed
Isoform #Evidence
Start_not_found Int
End_not_found
Merge Text // ar2 270106 added by request for StLoius
Split Text // ar2 270106 added by request for StLoius
Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_seq // Wen [030804 krb]
Trans_target ?Gene_regulation XREF Trans_regulated_seq // Wen
Cis_target ?Gene_regulation XREF Cis_regulated_seq // Wen
Visible Gene UNIQUE ?Gene XREF Corresponding_CDS // when live
Gene_history UNIQUE ?Gene XREF Corresponding_CDS_history // when dead
Corresponding_transcript ?Transcript XREF Corresponding_CDS #Evidence // links CDS' to new-style ?Transcript objects, 1-to-1 relationship
Corresponding_protein UNIQUE ?Protein XREF Corresponding_CDS #Evidence
Corresponding_PCR_product ?PCR_product XREF Overlaps_CDS // added for PCR mappings [010419 dl]
Corresponding_oligo_set ?Oligo_set XREF Overlaps_CDS
Matching_cDNA ?Sequence XREF Matching_CDS #Evidence
Expr_pattern ?Expr_pattern XREF CDS
RNAi_result ?RNAi XREF Predicted_gene // Lincoln RNAi [001213 dl]
GO_term ?GO_term XREF CDS ?GO_code #Evidence
Variation ?Variation XREF Predicted_CDS // replaces Has_allele tag in ?Sequence
Microarray_results ?Microarray_results XREF CDS //added for Microarray_results
Reference ?Paper XREF CDS // added [011030 krb]
Provisional_description ?Text #Evidence
Detailed_description ?Text #Evidence
Concise_description ?Text #Evidence
Brief_identification UNIQUE ?Text #Evidence
Confidential_remark ?Text
SAGE_tag ?SAGE_tag XREF Predicted_CDS #SAGE_mapping_info
YH_bait ?YH XREF Bait_overlapping_CDS ?Text// for yeast two hybrid data
YH_target ?YH XREF Target_overlapping_CDS ?Text
3d_data ?3d_data XREF CDS
//Structure_data ?Structure_data XREF Corresponding_CDS #Evidence
Remark ?Text #Evidence
Associated_feature ?Feature XREF Associated_with_CDS #Evidence
Method UNIQUE ?Method
Tags not used
Expr_pattern
Provisional_description
Detailed_description
Concise_description
Confidential_remark
SAGE_tag
3d_data
Merge and Split under Properties can be removed Wash U no longer use them
Proposed Changes
Remove unised tags?
