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This help document answers the following questions:

• What can I find using the cDNA Clone Query Form?
• How do I use this query form?
• What values are acceptable in each of the fields?
• How do I interpret the query results summary?
• How can I view a more detailed result?
• How do the detail results appear?
• Are there examples of queries and results?

See also:

• MGI Glossary (for acronyms, unfamiliar terms, or terms with unique usage at MGI)
• General Search Tips
• Wildcard Tips

What can I find using the cDNA Clone Query Form?

Use this form to search for expression information based on the tissue or cell line origin of the cDNAs.

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How do I use this query form?

To search for detailed data using this query form, enter or select values in one or more of the query form fields described in the following paragraphs. After entering values in the form fields, click Search to submit the query. Click Reset to clear the fields and return any default values. See Using MGI Query Forms for answers to questions such as:

• How do I submit a query?
• What are operators and how do they affect my query?
• How do I select more than one item on a list?
• Does it matter what case I use when I type values in the fields?
• How do the sort options work?
• Is there a maximum number of results I can get back all at once?
• Is there a way to speed up a query?
• When I enter exact marker or gene symbols in the Marker Range boxes, do the query results include or exclude those markers?

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What values are acceptable in each of the query form fields?

Gene Symbol/Name | Chromosome(s) | Genome Coordinates | Cytogenetic Band | Marker range | cM Position | | Gene Ontology (GO) Classifications | Type | Age | Cell Line | Tissue | Clone collection | cDNA Clone Accession ID | Return data type | Sort by | Maximum Returned

Gene/Marker	Symbol or name for a mouse genetic marker. Enter one or more terms, separated by commas (example: kit, bmp6, shh). Note: If the term itself contains a comma, put the entire term in quotation marks to ensure that the search is on the exact phrase (example: "cyclin B1, related sequence"). By default, the search is on current symbols/names and synonyms. However, you can limit your search to current symbols (no search of names) or current symbols/names only (no search of synonyms) The operators present additional search options; the default operator is contains. See How Operators Work on MGI Query Forms for more information.
Map position	Use these map position parameters (Chromosomes, Genome Coordinates, Cytogenetic Band, Marker Range, cM Position) to limit the scope of retrieved sequences to those associated with mapped genes and markers. When using chromosome(s), you can also define genome coordinates, cytogenetic band, or cM position. You cannot combine genome coordinates, cytogenetic band, and cM position with one another. You can enter MIT marker(s) in the marker range field(s) (e.g., between D6Mit128 and D6Mit129). See Using Map Position Fields on MGI Query Forms for complete details about entries for these fields.
Gene Ontology classification	Genes may be described using three broad categories reflecting biological roles: Molecular Function, Biological Process, or Cellular Component. The Gene Ontology (GO) Consortium has developed structured vocabularies to specify detailed aspects within each category. MGI uses GO terms to annotate gene records. See Using Gene Ontology Classification Fields on MGI Query Forms for details.
Clone source	The Clone source fields (Type, Age, Cell Line and Tissue) refer to the origin of the cDNA clone. Use them to search for source-related expression information. Note: The organism of origin is always mouse. Type Select clones from either in vivo material or in vitro material or Both. The default is in vivo. Note: If you select in vivo, cell line does not apply to your search; if you select in vitro, age does not apply. Age Use this field when searching for cDNA clones that are in vivo in origin. For Embryonic, click either Any (to query for embryonically derived cDNAs of any age) or enter day values in the two boxes (0 to 21). For Postnatal, click either Any (to query for postnatally derived cDNAs of any age) or enter values in the two boxes and click day, week, month, or year on the drop-down menu. Some age assignments do not have explicit numerical values. Therefore, for the purposes of querying, we have assigned them values. For instance, embryonic = embryonic day 0-21; postnatal = postnatal day 0-1825; postnatal newborn = postnatal day 0-4; and postnatal adult = postnatal day 21-1825. Therefore, if you query by ages that overlap these values, you will return them as well. Some clones have an age value of Not specified because the researchers did not supply the age. Those clones are excluded from query returns when you specify embryonic or postnatal age values. Cell Line Use this field when searching for cDNA clones that are in vitro in origin. There are three options. You can: Select one or more items from the list of cell lines that major publicly available cDNA libraries have been generated from Type in the name, or part of the name, of a cell line not found on this list into the Other field and select an operator from the drop-down menu (the default is contains). Combine options 1 and 2 in your query. Tissue There are three options. You can: Select one or more items from the list of tissues that major publicly available cDNA libraries have been generated from. Type in the name (or part of the name) of a tissue not on this list into the Other field and select an operator from the drop-down menu. Combine options 1 and 2 in your query. A link to the complete list of mouse tissues (origin of cDNAs) appears beneath the Tissue field.
Clone collection	To restrict your search to cDNAs with a clone ID, select one or more of the clone collections from the selection list. (For details about the differences between the sets on this list, see MGI Clone Collections.) Select ANY if you do not want to restrict the search by clone collection.
Accession ID	A cDNA clone record may be associated with several Accession IDs including an MGI Accession ID, GenBank ID, and so on. You can search by any accession ID assigned to a cDNA clone.  See Using the Accession IDs Query Form for details on searching by accession ID.
Sorting and output format	The Sorting and output format fields let you determine the order and content of query summary results as well as to limit (or expand) the amount of data to display. Return data type Click either clones with sequence database links or all clones Sort by The sorts are alphanumerical. Click one of the choices (tissue - the default, gene symbol, age) to determine which feature your results are sorted by. Maximum Returned The default is 500. You can change this number to whatever you wish or you can click no limit.

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How do I interpret the query results summary?

The summary results for a cDNA clone query (or when linking from a marker detail page) comprise the following columns: Nucleotide Probe/Clone AccID, Name, Clone Collection, Age, Tissue, Cell Line, Gene. See What values are acceptable in each of the fields? for descriptions.
(PUTATIVE) appearing after the gene symbol means that the relationship between the gene and clone is established by computation rather than experimental data.

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How can I view a more detailed result?

The summary listing provides a link to the detailed cDNA clone record through the Nucleotide Probe/Clone AccID. Click the desired Gene symbol to see its detailed gene record.

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How do the detail results appear?

The detailed results for molecular probes and Clones have the format described in Using the Molecular Probes and Clones Detail Report.

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Are there examples of queries and results?

In following examples, we list the field values required for each query result; if a value is not listed, the default is assumed.

1. List all the genes on Chromosome 4 for which cDNAs have been isolated from the kidney.
   Sort by   Gene Symbol
   Chromosome(s)   4
   Tissue   kidney

2. For the gene Lepr, show the complete list of cDNA clones and the tissues from which they have been isolated.
   Sort by  Tissue
   Gene Symbol/Name   BEGINS lepr
   

3. What genes are expressed (according to cDNA clone data) in brain during embryonic development in the period of 10-15 days after conception?
   Sort by   Gene Symbol
   Type  in vivo
   embryonic day  10 to 15
   Tissue  brain

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