WormBase Model:Clone

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WormBase Models

Curator Comments/Description


// ?Clone class

?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 
                                                // pMap units are bands
                  Clone_left_end ?Sequence      // filled by XREF
                  Clone_right_end ?Sequence     // filled by XREF
                  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
        Sequence    ?Sequence XREF Clone
        PCR_product ?PCR_product XREF Clone
        Length  Seq_length UNIQUE Int                   // bp
                Gel_length UNIQUE Float                 // Kb
        Location ?Laboratory #Lab_Location
        URL Text                          // to link to MRC_geneservice website ar2
        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 
                                // start and stop offsets from self start
                        Bands   UNIQUE Int UNIQUE Int
                        Gel ?Motif  #Lane               // Magic tag2 construct
        Contig9 Chromosome UNIQUE ?Map 
                Vaxmap UNIQUE Float
                In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
                Flag    UNIQUE Int
        Expression_construct    Pattern ?Text   // archaic
        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 UNIQUE ?Accession_number XREF Clone // added [031120 krb]
        Type UNIQUE Cosmid            // 000824 Lincoln's additions to segregate clones
                    Fosmid            // added 06/12/01 by krb for dl
                    Other Text        // added to catch all clones 011017 dl
        Transgene ?Transgene XREF Clone
        Derived_from    ?Clone

Proposed Changes

unused tags












Class contents WS242

215788 Objects/Object references.

Fosmids: 15355 Don Moreman 1738 C. elegans genomic

Cosmids: 17887 Cosmids -> Cosmid Tag 5548 Other elegans cosmids 7 Other clones C. elegans? 2 BACs clones C. elegans?

YACs: 585 C. elegans YACs

cDNA 142175 Yugi Kohara EST clone objects. 2590 Stratagene ESTs CEE* CEM* 1380 OST 1645 Chris Martin C. elegans EST project cm* 40 UofArizona WASHU C. elegans EST project ca* 326 Unknown EST project CES* 48 Cadmium Response gene ESTs DDRT* VL*

Plasmids: 20256 sjj PCR product clone 411 Other plasmids

   289 from Expression_patterns
   13 C. elegans genomic
   108 Variety of sources Fire Vector Kit etc.

17 Brugia contig clones via Positive_gene ?Gene connections. 11 Briggsae contig clones via Positive_gene ?Gene connections. 62 Brenneri contig clones via Positive_gene ?Gene connections. 5 Japonica contig clones via Positive_gene ?Gene connections. 7 Remanei contig clones via Positive_gene ?Gene connections.