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Tips on Finding cDNA Clones

Many Clones Are Available

To accelerate the pace of biomedical research, tens of thousands of cDNA and expression clones have been assembled into collections that are readily available to the scientific community. Before setting out to construct and characterize a new clone, it is worth a few minutes at the computer to see if one already exists.

Finding Clones for a Gene

When searching the NCBI Gene Database, look for "NIH cDNA clone" hypertext links, which lead to one or more cDNA sequences. Similar links may be found on protein and UniGene entries.

In the full report for a gene, look in the "Links" section on the right for possible MGC clones.

Searching for Clone Sequences

In addition to finding cDNA clone sequences by following links from the Gene report, the Nucleotide sequence database may be searched directly. When doing this, it is useful to include "MGC" qualified as a keyword to limit the results to sequences of clones from the MGC collection. For convenience, clones from the ZGC and XGC collections also have "MGC" as a keyword. Try the following sample queries.

Search for: MGC[Keyword] AND apoptosis
Search for: MGC[Keyword] AND AMID[Gene Name]
Search for: MGC[Keyword] AND Xenopus laevis[Organism]

Clone Sequence Entries

After finding a cDNA sequence of interest, examine the COMMENTS section for general information on availability.

Clone identifiers and other specific information are in the FEATURES section under "source".

Using LinkOut

Clone distributors are encouraged to use the NCBI's LinkOut system to provide links to online order forms or other information. LinkOut is a generic mechanism for attaching links to any NCBI database object, such as a gene or a sequence. To see if LinkOut information exists, click on the word "Links" (see graphic) and look for LinkOut on the drop-down menu.

In this example, three of the cDNA clone distributors (Geneservice Ltd., Open Biosystems, and RZPD) have provided links to their sites for online ordering. Links for other types of reagents (such as probes and primers) may also be present.


Mammalian Gene Collection

The NIH Mammalian Gene Collection (MGC) project aims to identify at least one full-ORF cDNA clone for each human and mouse gene, produce a high-accuracy sequence, and make the physical reagents easily available to researchers. The collection is augmented by a limited number of rat cDNAs and non-mammalian clones coming from the affiliated Zebrafish (ZGC) and Xenopus (XGC) projects.

MGC Homepage
ZGC Homepage
XGC Homepage

I.M.A.G.E. Distributors

The I.M.A.G.E Consortium, headquartered at Lawrence Livermore National Laboratory, has handled clone arraying, archiving, and distribution for a number of large-scale projects, including MGC and The ORFeome Collaboration.

I.M.A.G.E. Homepage

Distribution of the physical reagents, either individual clones or entire collections, is handled by the following U.S. and European suppliers:

American Type Culture Collection
Invitrogen, Inc.
Open Biosystems
Geneservice, Ltd.
RZPD German Resource Center

Other Clone Collections

A number of international efforts are under way to identify and sequence full-length cDNA clones. Policies on reagent availability vary, so refer to the individual project sites for details.

German Human cDNA Project
Kazusa cDNA Project
NEDO Human cDNA Sequencing Project
DKFZ Pongo pygmaeus cDNA Project
RIKEN Mouse Gene Encyclopedia Project
NIA Mouse cDNA Project
Berkeley Drosophila Genome Project
RIKEN Arabidopsis Full-Length cDNA Project

What Is LinkOut?

LinkOut is a feature of the NCBI Entrez system that allows links to any web resource to be attached to any database entry. This allows users to find relevant biological materials, research tools, full-text publications, consumer health information, and more.

General LinkOut Information
Information for LinkOut Providers

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