Gene Trap Questions and Answers
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This help document answers the following types of questions about gene traps.

General questions about gene traps

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What is gene trapping?

Gene trapping is a high-throughput approach used to introduce genome-wide insertional mutations.

Gene trap experiments in embryonic stem (ES) cells produce mutant cell lines in which integration into a putative gene is selected by expression of a selection gene in ES cells. The trapped gene is usually (though not necessarily) mutated by the integration, altering either the gene expression or the protein product produced. The site of integration can be characterized by cloning, extension of cDNA products, or direct sequencing of the insertion site.

See also:

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How are gene trap alleles named?

Once a gene trap cell line is isolated and the insertion site identified, a gene trap mutant cell line designation is used to create an allele symbol.

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Who are the cell line creators?

Creator Abbreviation Lab Code / Name (ILAR) 1 Cell Line ID (Creator) Sequence Tag ID (Creator) Seq ID (GenBank) Nomenclature Example
BayGenomics BG Byg / BayGenomics XH152 XH152 CC199534 Alms1Gt(XH152)Byg
Centre for Modeling Human Disease CMHD Cmhd / Centre for Modeling Human
Disease
CMHD-GT_141.1H7-3CMHD-GT_141.1H7-3CL706334Etv2Gt(CMHD-GT_141.1H7-3)Cmhd
Exchangeable Gene Trap Clones EGTC Imeg / Institute of Molecular Embryology and GeneticsAyu21-B196Ayu21-B196AB299416Adipor2Gt(Ayu21-B196)Imeg
Embryonic Stem Cell Database ESDB Mfgc / Mammalian Functional Genomics Centre PST11001 PST11001CZ192167AtrxGt(PST11001)Mfgc
Fred Hutchinson Cancer Research Center FHCRC Sor / Philippe SorianoFHCRC-GT-S20-7E1FHCRC-GT-S20-7E1CL706141Chd7Gt(FHCRC-GT-S20-7E1)Sor
German Gene Trap Consortium GGTC Wrst / German Gene Trap ConsortiumW223E05W223E05CL215544Gnl3Gt(W223E05)Wrst
Lexicon Genetics N/A Lex / Lexicon Genetics OST179231OST179231CG559761Pomgnt1Gt(OST179231)Lex
Sanger Institute Gene Trap Resource SIGTR Wtsi / Wellcome Trust Sanger InstituteBC0122BC0122CZ259233Atg16l1Gt(BC0122)Wtsi)
Telethon Institute of Genetics and Medicine TIGEM Mist / Telethon Institute of Genetics and Medicine GC0844 GC0844 CW020574 Gt(GC0844)Mist
Texas A&M Institute for Genomic Medicine TIGM Tigm / Texas A&M Institute for Genomic Medicine IST10006D1 IST10006D1BBF1 EF717953 Slc25a40Gt(IST10006D1)Tigm
Velocigene2 N/A Vlcg / Velocigene 11648B-F7 N/A N/A Abcb9tm1(KOMP)Vlcg

Notes:

  1. Institute for Laboratory Animal Research (ILAR)
  2. This organization provides targeted mutant cell lines.

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Is there a way to tell which group created a mutant ES cell line?

If MGI has evidence from a publication or from direct submission, you can determine the ES cell line creator. On a Gene-trapped Allele Detail report, locate the Mutation Origin section. The creator name appears in parentheses beside Mutant Cell Line. The creator information also appears in the Nomenclature section as part of the allele symbol and name. See Who are the cell line creators? for additional information about creator abbreviations, lab codes, and cell line IDs.

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How can I determine if an ES cell line has been made into a mouse?

  1. Locate the Mutation Origin section of a Gene-trapped Allele Detail report.
  2. If MGI has a paper containing evidence that the cell line has been made into a mouse, Germline Transmission: and Earliest citation of germline transmission plus a citation appears. Click the J: number to access MGI Reference Query Results for complete details on the paper.

Note: The Find Mice (IMSR) section of the Gene-trapped Allele Detail report contains information on this topic. See How can I tell if a cell line or a mouse strain carrying the mutation is available for purchase? for an example.

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How can I tell if a cell line or a mouse strain carrying the mutation is available for purchase?

Locate the Find Mice (IMSR) section of a Gene-trapped Allele Detail report. The information indicates whether or not mouse strains and cell lines are available from the International Mouse Strain Resource (IMSR).

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How can I identify a gene trap mutant ES cell line ID?

mutant cell line

See the table at Who are the cell line creators? for examples of additional accession identifiers associated with cell lines.

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Is there a list of all gene trap cell line accession IDs?

Yes. Click Download-->MGI Data and Statistical Reports--> to access MGI Marker associations to Gene Trap IDs (tab-delimited).

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Is there a list of all IDs and nomenclature associated with gene traps in MGI?

Yes. Click Download-->All MGI Reports--> to see all gene traps associated with markers.

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Searching for gene trap or cell line data

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Where can I find gene trap and/or cell line data?

MGI incorporates mouse cell line and gene trap sequences for almost all gene traps in dbGSS including IGTC and Lexicon Genetics gene traps, and TIGM. The International Gene Trap Consortium (IGTC) houses publicly available gene trap cell lines available upon request.

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How can I find all the available sequence-tagged gene traps from a specific creator?

Use the MGI Phenotypes, Alleles, & Disease Models Query Form.

  1. Enter the provider's ILAR-designated lab code in the Allele field (in the Nomenclature & Location section). Examples: Imeg (Institute of Molecular Embryology and Genetics - EGTC) or Wtsi (Wellcome Trust Sanger Institute). Leave the default (contains).
  2. Click gene trapped (in the Categories section).
  3. Click no limit in the Sorting and output format section.
  4. Click Search. The result is a Phenotypic Alleles Query Results -- Summary of all gene traps containing your character string entry. Note that you can also find affected anatomical systems and genetic backgrounds of interest in this report.

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Can I search for all gene traps or only for those that have been made into mice?

Both searches are possible. You can customize your search to include all gene traps or only those made into mice.

To include all gene traps:

To include only gene traps made into mice:

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What are the ways of searching for gene trap insertions?

  1. You can use the Phenotypes, Alleles, & Disease Models Query Form to search for gene trap insertions:
    • By phenotype
      1. In the top row, next to Mouse phenotypes & mouse models of human disease, enter phenotype terms in the Phenotype/Disease box. (The Select or Browse links provide lists or structures or ontologies to choose from.)
      2. In the third row beside Categories, click the box beside gene trapped.
      3. Make any other selections as desired (e.g., you can limit the number of items returned and determine how the results are sorted).
      4. Click Search to begin and/or Reset to refine any results.

    • By nomenclature
      1. Enter the symbol, name, or synonym of a known mouse gene to find any associated gene traps.
      2. Click gene trapped (in the Categories section).
      3. Click Search.

    • By chromosomal location
      1. In the Nomenclature & location section, click the chromosome of the associated marker and enter additional information as desired in the Cytogenetic Band, cM Position, or Genome Coordinates boxes.
      2. In the Categories section, click gene trapped.
      3. Click Search.
      4. Note: The MGI gene trap algorithm restricts the search to gene traps with marker associations; a chromosomal location search therefore cannot return gene traps without those associations. Thus, when there is no marker association for the gene trap, a search by location from the Phenotypes, Alleles, & Disease Models Query Form does not yield a result. However, if you know a landmark or a region, try entering this location in MGI's GBrowse and clicking the GeneTraps_RNA_tags and GeneTraps_DNA_tags tracks. (See How can I tell if a given gene trap has trapped a gene? and How do I interpret GBrowse gene trap tracks? for additional information about GBrowse.)

    • By category
      1. In the Categories section, click gene trapped.
      2. By default, this query queries returns all gene traps (cell line and mouse line). If you want to limit this search to cell lines made into mice, click Exclude allele records present only in cell lines.
      3. Click Search.

  2. You can use the Quick Search box (at the top of every MGI page) and enter:
    • the nomenclature (symbol, name, synonym) for a gene or an allele or a creator/provider abbreviation (see Who are the cell line creators? for a list).
    • an accession identifier (mutant cell line ID, provider ID, GenBank sequence tag ID). Summary reports return links to any associated MGI detail pages.
    • only the cell line designation to find gene trap alleles not located in a known gene.

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Where can I find vector information?

The Gene-trapped Allele Detail report provides the name, type, and description of the vector used for a gene trap event if available.

Locate Mutation description--> Mutation. If there is vector information available, it appears on the Mutation line.

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Can I use the MGI Batch Query to find gene traps?

No. The ability to enter a group of cell line accession IDs and return information about corresponding gene traps may be available in a future MGI release.

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I search using a gene trap ID (or nomenclature) but get no marker results. Why not?

There may be several reasons for not getting expected results:

  1. The gene trap is not in GenBank.
  2. The gene trap is in GenBank, but it is not from one of the established creators (see Who are the cell line creators? for a list).
  3. There is no gene-trap-to-gene association for the gene trap.

If you are using the Quick Search tool, a link to the allele detail may appear in the Other Results by ID section of the Quick Search Results. You can also try entering a landmark or a region in GBrowse and clicking the GeneTraps_RNA_tags and GeneTraps_DNA_tags tracks. (See How can I tell if a given gene trap has trapped a gene? and How do I interpret GBrowse gene trap tracks? for additional information.)

See Why aren't all gene traps associated with a gene? for more details.

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Finding gene associations

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How can I find all the gene traps associated with a given gene?

  1. You can use the MGI Quick Search tool:
  2. You can use the MGI Phenotypes, Alleles, & Disease Models Query Form. Enter the gene nomenclature and follow the appropriate links.
  3. You can look through the MGI Marker associations to Gene Trap IDs report to locate the gene and its traps.

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How can I find all genes associated with gene trap insertions?

Click Download-->MGI Data and Statistical Reports--> to access MGI Marker associations to Gene Trap IDs (tab-delimited) for this list.

  1. On the Phenotypes, Alleles, & Disease Models Query Form, locate the Categories row.
  2. Click the box beside gene trapped.
  3. Click Search. A Phenotypic Alleles Summary report appears, identifying the number and name of all genes associated with gene trap insertions.

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Why aren't all gene traps associated with a gene?

MGI does not establish gene trap-to-gene associations:

  1. where sequence tags for a gene trap allele overlap multiple genes in the trapped gene orientation:
          
    	->
         ----->
           ------>
         ---------------
    
  2. where sequence tags for a gene trap allele overlap one or more genes in reverse orientation (not disrupted by the gene trap mechanism):
           
    	<-
            ----->
         --------------
    
  3. where sequence tags for a gene trap allele overlap no known genes using current gene model coordinates:
    	 ->
         --------------
    
  4. where gene trap sequence tags for an allele do not align with the reference mouse genome:
    
         ---------------
    
  5. where gene trap sequence tags for an allele align equally well to multiple locations:
         ChrA     1->                 
          --------------
    
         ChrB         1->                 
          ---------------
    
  6. for mixed cell lines, characterized by multiple sequence tags for the same cell line that have good alignments to different locations in the genome:
         ChrA    1->(MCL:xyz1)
          -------------------
          
         ChrB      2-> (MCL:xyz1)
          -------------------
          
Legend:
->	     Gene Trap Sequence Tag aligned to the genome. The arrow indicates gene trap polarity.
Numbers      Indicate tag identities.
MCL	     Indicates Mutant Cell Line identity.
-----> 	     Known gene aligned to the genome. Arrow indicates transcriptional polarity.
-----------  A location in the reference mouse genome. For multiple locations, different chromosomes are indicated.

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How can I find genes near a gene trap not associated with a gene?

If the Gene-trapped Allele Detail report displays a genome browser link, you can view gene trap sequence tag positions relative to genome coordinates.

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How can I find gene traps not associated with a gene but that are near a gene of interest?

genome context

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Can I search for gene traps where no known genes exist?

No. However, MGI's GBrowse provides views of gene trap sequence tag positions relative to genome coordinates. See Can I view the approximate locations of gene trap insertions? for how to access this genome browser. See How can I tell if a given gene trap has trapped a gene? and How do I interpret GBrowse gene trap tracks? for additional GBrowse information.

Note: You can find any gene trap, regardless of gene association, by using its mutant cell line ID, provider tag ID, or GenBank sequence tag ID.

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Can I use a marker detail report to determine how many gene traps are available as ES cell lines only, as both cell lines and mice, or as mice only?

Not currently. This may be available in the future in a public report.

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Searching for sequence information

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Where can I find sequence tag identifier(s)?

  1. Locate the Mutation description row on a Gene-trapped Allele Detail report.
  2. Click the icon () next to Sequence Tags.
    In the table that appears, the GenBank ID column lists the GenBank sequence tag ID for each gene trap insertion.
    The Tag ID column contains the sequence tag identifiers.
    The sequence tag's GenBank identifier (GenBank ID), the sequencing technique (Method), and chromosome, map position, and strand (Tag Location) also appear. Note that you can select sequences here to download in FASTA format or forward to MGI's MouseBLAST program.

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Is there a way to determine sequence tag orientation?

Yes.

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Is is possible to tell whether a sequence tag defines the insertion site (is a genomic- or DNA-based tag) or not (is an RNA-based tag)?

Yes. On a Gene-trapped Allele Detail report, click the icon () next to Sequence Tags. The table that appears contains a Method column where the information you are looking for appears (if known). If the method is 3' RACE or 5' RACE, the tag defining the insertion site is RNA-based. Any other method listed is DNA- (or genomic-) based (for example, inverse PCR, 3' or 5' splinkerette, plasmid rescue).

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Where can I find the coordinates and strand for a given gene trap sequence tag?

The Gene-trapped Allele Detail report displays this information for any gene traps that map to a single position in the mouse genome.

See the previous image for an example of the information in the Tag Location (strand) column.

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Can I view coordinates/strands for all significant sequence tag BLAST hits for mixed cell line gene traps that map to multiple locations?

Yes. When the Mutation description section (next to Mutation) of a Gene-trapped Allele Detail report indicates that sequence tags for an insertion align in multiple locations:

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Can I download the sequence tag for a gene trap insertion in FASTA? Can I send it to MouseBLAST?

Yes. This option is available on the following MGI reports:

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Can I find gene trap insertions by BLASTing against gene trap sequences and searching by sequence similarity?

Yes. Use MGI's MouseBLAST. BLAST results link to corresponding MGI Alleles and Genes. See Using MouseBLAST - Overview for how to use this tool.

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Can I view the approximate locations of gene trap insertions?

Yes. Both the Gene-trapped Allele Detail report and the MGI genome browser (GBrowse) provide views of gene trap sequence tag positions relative to representative gene transcripts.

In the Mutation description section, click the icon (click the icon () next to Genome Context. To access the GBrowse view, click View all gene trap sequence tags in this region at the bottom of the image that appears.

See How can I tell if a given gene trap has trapped a gene? and How do I interpret GBrowse gene trap tracks? for additional information.


For gene trap alleles not associated with markers, click View all gene trap sequence tags within a 10kb region to access the GBrowse view. The display shows a 5kb region on either side of the gene trap sequence tag.

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How do I interpret GBrowse gene trap tracks?

GeneTraps_per_Gene track

This color-coded gene trap frequency track for MGI genes indicates the number of insertions per gene. Only insertions that "trap" a gene (i.e., overlap the gene's coordinates in the correct transcriptional orientation) are counted.

See also How can I tell if a given gene trap has trapped a gene? for additional information.)

Gene model colorNumber of gene traps associated with the marker
RedMore than 1000
Orange101 - 1000
Green11 - 100
Blue2 - 10
VioletOne
BlackNone

GeneTraps_RNA_tags track

These gene trap sequence tags from GenBank dbGSS have an RNA-based sequence tag method (5'-RACE or 3'-RACE).

Sequence tag methodInsertion site in the intron
5'-RACE (blue)Downstream from the most 3' exon represented in the sequence tag
3'-RACE (green)Upstream from the most 5' exon represented in the sequence tag

GeneTraps_DNA_tags track

These gene trap sequence tags from GenBank dbGSS have a DNA-based sequence tag method.

How can I tell if a given gene trap has trapped a gene?

If the MGI allele_detail page has an association for the gene, and in MGI GBrowse,

then the gene trap has trapped a gene.