WormBase Model:Transcript

WormBase Models

Model

///////////////////////////////////////////////////////////////////
//
// ?Transcript class - krb 021126
//
///////////////////////////////////////////////////////////////////

?Transcript     Evidence #Evidence
                SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transcript
                Structure Source_exons Int UNIQUE Int
                DB_info DB_remark ?Text #Evidence // was missing from first draft of Transcript class krb
                        Database ?Database ?Database_field UNIQUE ?Text
                Origin  From_laboratory UNIQUE ?Laboratory                         // [020306 kj]
                        Species UNIQUE ?Species                                    // [020306 kj]
                Visible Gene ?Gene XREF Corresponding_transcript // for live transcripts
                        Gene_history UNIQUE ?Gene XREF Corresponding_transcript_history // when Transcript is dead
                        Variation ?Variation XREF Transcript // added to fit two alleles of RNA genes [021127 krb]
                        Matching_cDNA ?Sequence XREF Matching_transcript #Evidence            // to attach non-coding RNA genes to matching ESTs
                        Corresponding_CDS UNIQUE ?CDS XREF Corresponding_transcript #Evidence // 1-2-1 relationships with coding genes
                        Corresponding_PCR_product ?PCR_product XREF Overlaps_transcript
                        Corresponding_oligo_set ?Oligo_set XREF Overlaps_transcript
                        Reference ?Paper XREF Transcript                           // [020306 kj]
                        RNAi_result ?RNAi XREF Transcript //was missing from model [021126 krb]
                        GO_term ?GO_term XREF Transcript ?GO_code #Evidence // [030411 krb]
                        Microarray_results ?Microarray_results XREF Transcript      //added for Microarray_results
                        Provisional_description ?Text #Evidence
                        Detailed_description ?Text #Evidence
                        Concise_description ?Text #Evidence
                        Brief_identification UNIQUE ?Text
                        Confidential_remark ?Text
                        SAGE_tag ?SAGE_tag XREF Transcript #SAGE_mapping_info
                        RNASeq_FPKM  ?Life_stage  Float  #Evidence
                        Remark ?Text #Evidence
                Properties Transcript UNIQUE  asRNA UNIQUE Text
                                              lincRNA UNIQUE Text          // lincRNAs 
                                              mRNA UNIQUE Processed_mRNA
                                                          Unprocessed_mRNA
                                              miRNA UNIQUE Text            // [020306 kj]
                                              ncRNA UNIQUE Text            // true non-coding RNAs
                                              piRNA UNIQUE Text            // 21U-RNA/piwi-interacting RNA/piRNA Gary W. WS228
                                              rRNA UNIQUE Text
                                              scRNA UNIQUE Text
                                              snoRNA UNIQUE Text           // [030102 krb]
                                              snRNA UNIQUE Text
                                              snlRNA UNIQUE Text           // small nuclear like 
                                              stRNA UNIQUE Text            // [010723 dl]
                                              tRNA Type UNIQUE Text        // ck1 [030926] krb
                                                   Anticodon UNIQUE Text   // 
                           Isoform #Evidence                               // Set if this is a RNA isoform
                           Ignore #Evidence                                // Set for putative NMD targets which we do not want to see in wormrna
                           Start_not_found                                 // [020306 kj]
                           End_not_found                                   // [020306 kj]
                Associated_feature ?Feature XREF Associated_with_transcript #Evidence
                Method UNIQUE ?Method                  

Proposed Changes

Unised tags

---

Start_not_found #acedb magic tag

End_not_found #acedb magic tag 
 
GO_term
 
Provisional_description 

Detailed_description

Concise_description