Description of Fields For 15k Annotation File

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• Daughter- Rearrayed clone name

• Parent- Source Clone name

• FullSeq- Value=’Y’ indicates full sequence for the clone is available. 3’ sequence and 5’ sequence assembled using Phred/Phrap system. This field has a link to the sequence pages for the cDNAs of interest.

• 3’ Verified- the 3’ sequence of the Daughter clone shows sufficient homology to the 3’ parent clone to verify the sequence. Values are ‘Y’= verified, ‘U’= Unvarifiable, <blank>=not verified, ‘O’=Orphan. An Orphan is any clone which has been sequence verified by multiple sequences obtained from the daughter clones, but does not match the sequence of the parent clone.

• 5’ Verified- the 5’ equence of the Daughter clone shows sufficient homology to the 3’ parent clone to verify the sequence.

• Clone Verified- Either the 3’ sequence or the 5’ sequence show sufficient homology to verify the address of the clone is correct. This field has a link to the sequence verification pages (with an arrow pointing at your clone of interest).

• Mitochondrial- The clone shows significant homology to the mitochondrial genome.

• Clone Description- Based on BLAST against the GenBank nr repository. The Clone Description is taken from the descriptor on the higher scoring hit to either the 3’ sequence or the 5’ sequence as long as the Score > 100. See "Homology Rank" below.

• Desc Source-Indicates which sequence (3’ or 5’) was used as the query for determining the description. 3’ and 5’ sequences are always indicated with a "-3" or a "-5" attached to the clone name, respectively. This field is a link to the sequence page.

• Hit #- Indicates which of the top 20 hits (stored in our database) is the descripter for ‘Description’ field.

• Score- Indicates similarity between the ‘Description’ sequence and the ‘Desc Source’ sequence. This "modified BLAST score"  is a composite of the BLAST scores returned for each alignment.

• Homology Rank- defined as follows:

  ‘Score’ <100             à  Unknown. Value of field left blank

  100< ‘Score’ < 200   à  Weak

  200 < ‘Score’ < 400  à  Moderate

  ‘Score’ > 400             à  Strong

• Database- the query database.

• Species- The species in which one can find ‘moderate’ or ‘strong’ scoring hits to genes.

• Function- Human curated classification of function.

• Hits to Genomic- Indicates whether a ‘moderate’ or ‘strong’ homology to some type of genomic sequence exists.

• Unigene- NCBI unigene ID. Based on Parent clone 3’ sequence membership in NCBI UniGene cluster. This field is a link to the NCBI Unigene cluster.

• HomoloGene- ID’s based on tagging of NCBI Unigene. This link allows the user to find information regarding homlogous genes found in other species.

• GeneCards- ID’s based on tagging of NCBI Unigene.

• LocusLink- Link established to LocusLink by Parent clone NCBI Unigene membership.

• CGAP- Link to CGAP established through Parent clone GenBank accession number.

• TIGR- Link TIGR gene indices established through Parent clone GenBank accession number.

• MGI- Link established to the Mouse Gene Informatics at the Jackson Laboratory through Parent clone GenBank accession number.

• GO Tag - Link to the Gene Ontology Corsortium IDs established by Parent clone NCBI Unigene membership.

• GO Description- Description given to the GO tag by the Gene Ontology Consortium.

• NIA- Links to the MGI for those clones whose parent clones were mapped by Jackson Laboratory Backcross Panal.

• MRC-Links to UniSTS for those parent clones mapped by radiation hybrid by the UK Mouse Genome Centre.

• MIT- Link to MIT RH markers established by homology based comparison (BLAST score>200).

• NCBI Chromosome- Chromosome location based on Parent clone NCBI Unigene membership.

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