This help document answers the following questions about the Marker Detail Report.
The title of this report describes the genomic feature type returned as a result of your query. The details may be for a gene, a DNA segment, a QTL, a microRNA, a pseudogene, a cytogenetic marker, a BAC/YAC end, a complex/cluster/region or some other genome feature.
Depending on data availability and the marker type, this detail report contains information in some or all of the following categories:
| Field |
Description |
Symbol
Name
ID |
Official gene symbol for the mouse genetic marker. If the symbol is unofficial, the word interim follows the symbol name, in parentheses, to indicate that the nomenclature is being reviewed by the Mouse Genomic Nomenclature Committee.
The name for this marker appears beneath the symbol. A symbol may be a gene, DNA segment, QTL, cytogenetic marker, pseudogene, BAC/YAC end, complex/cluster/region, or one of the other genome features including endogenous viruses, retrotransposons, integration sites, and repetitive elements. An additional class of such features includes genomic segments that function or are biologically significant as DNA elements.
The MGI accession identifier appears beneath the name.
If there is historical data for this marker in MGD, a link to a Nomenclature History report appears on the right.
|
| STS |
If applicable, symbols for sequence tag sites (STS) with the same DNA sequence (or a portion of that sequence) as the marker, linked to the DNA Detail Segment Detail page. For example, D7Mit19 and D7Mit31 are said to be STSs of Tyr. |
| Synonyms |
Names or symbols for a given marker that may appear in the literature but which are not approved names or symbols. |
| Genetic Map |
As much as is known for this marker of the following:
- Chromosome to which the marker is assigned. Aside from a chromosome number, other possible values include MT (mitochondrial), XY (XY pseudoautosomal), UN (chromosome assignment is not known).
- Centimorgan position. For markers whose position is known, a numeric value appears. This value is calculated from various MGI-stored values, including those derived from experimental results, Chromosome Committee Reports, and MIT Mouse Genome project downloads. For QTLs, the numeric value is the position of the peak correlated region/marker. Markers assigned to a chromosome where a position is not yet estimated appear as syntenic.
- Cytogenetic position.
|
| Sequence Map | Appears if coordinates are assigned and includes:
- genome coordinate range and strand, in base pairs from VEGA annotation (selected as genomic representative sequence)
- external links to other genomic context displays (e.g., Vega ContigView, Ensembl ContigView, UCSC Browser, NCBI Map Viewer)
- On the right, a thumbnail image link to the MGI Mouse Genome Browser display for the marker's coordinates. You can also click MGI Mouse Genome Browser for a full-page display.
Note: If the information you expect to see does not appear in the Mouse Genome Browser (or other browser) display, you may need to turn on (i.e., click) the viewing aides (i.e., tracks, features, maps) in the various displays.
|
|---|
Mammalian
homology |
Mammalian homology records for this marker, as follows (depending on availability):
- A list of species with curated orthology relationships with (in parentheses) a link to the MGI Mammalian Orthology Query Results page of curated orthology relationships
- A link to a mouse/human comparative map display of the area plus or minus 2 cM around the marker
- A link to the TreeFam database (phylogenetic trees of animal genes).
- A link to this marker's MGI Protein Superfamily Detail page if it can be annotated to a Protein Information Resource SuperFamily (PIRSF) classification name.
|
| Sequences |
| Representative Sequences |
Representative genomic (from the genome assembly), transcript, and polypeptide sequences for your marker and:
- the sequence ID (e.g., OTTMUSG00000009932)
- a link to the sequence provider (e.g., VEGA Gene Model)
- a link to the MGI Sequence Detail page
- Length: the sequence length
- Strain/Species: the sequence strain (or species, if other than laboratory mouse)
- Flank: If the marker has genome coordinates, you can add an equal amount of flanking sequence to either end when forwarding to MouseBLAST.
|
| For the selected sequences |
You can:
- download them in FASTA format
- forward them to MouseBLAST
- enter an amount of flanking sequence (if the marker has genome coordinates) and then download or forward to MouseBLAST.
- click the box beside each representitive sequence you want to download or forward OR click the number in parentheses next to All sequences and make your choices there.
|
| All sequences |
Link to the Mouse Sequence Summary Report for all sequences for your marker. This link appears if there is at least one sequence associated with a marker. |
Notes on representative sequence display:
- If there is no display, it means that a representative sequence could not be determined.
- Genomic: DNA sequence defined by genome coordinates assigned to marker, if any; otherwise, the longest DNA sequence associated to marker.
- Transcript: RefSeq (NM_) sequence if associated to a marker; otherwise, the longest GenBank RNA sequence.
- Polypeptide: The longest SWISS-PROT sequence; otherwise, longest TrEMBL sequence.
- If the strain/species is not specified, – appears.
- If the strain/species is not resolved, the original (provider) value followed by * appears. (Providers describe sequence attributes — strains/species, tissues, libraries, clone collections, and so on — in their reports. MGI captures these original values, converts them to MGI controlled vocabularies if possible, and stores them. Once captured, values are called resolved, and you can use them as search terms on the Mouse Sequence Query Form. If the original value is not resolved to a controlled vocabulary term, it does not produce results if queried upon, and the message to this effect appears on your query report.)
- Not applicable indicates that the value does not apply. For example, all DFCI, DoTS, or NIA Mouse Gene Index sequences display Not applicable in the Strain/Species column, and all RefSeq, DFCI, DoTS, NIA Mouse Gene Index, Ensembl, SWISS-PROT, and TrEMBL sequences display Not applicable in the Clone Collection column.
|
| Phenotypes |
Depending on availability, the display includes some or all of the following links or information. Numbers in parentheses indicate how many items each linked report contains.
- Separate links to a summary of either all, only targeted, only spontaneous, only chemically induced, or only other phenotypic alleles associated with this marker.
- A short summary of phenotypes produced by mutant alleles.
- Associated Human Diseases: a link to a list of all distinct human diseases where a mouse mutant allele of this gene is part of a mouse genotype that represents a disease model. (This does not necessarily mean that mutations in this gene contribute to or are causative of the disease.)
- Alleles Annotated to Human Diseases: a link to the Phenotypic Alleles
Query Results -- Summary page: alleles with OMIM annotations to associated genotypes
- Phenotype Images: Click the number to bring up the All Phenotype Images for Gene report and view every phenotype image that MGI has for this gene.
|
| Polymorphisms |
Links to the following MGI summary reports (the number available appears in parentheses):
- Polymorphisms Query Results -- Summary for any RFLPs/PCRs for this marker:
- Mouse SNPs Query Results -- Summary for any SNPs within 2 kb of this marker. Note: If MGI gene and marker genome coordinates are out of sync with the SNP data, within 2 kb of this marker does not appear, and the summary report indicates the discrepancy. See Understanding Mouse SNP Coordinate Discrepancies for details.
|
Gene Ontology (GO)
Classifications |
Links to GO annotations for a biological process, cellular component, and molecular function of the gene. To see all items, click All GO classifications (see Gene Ontology Classifications for how to interpret the fields on this page.) You can browse the GO vocabulary from this section of the query results and locate multiple terms that annotate a gene record. |
| Expression |
Depending on availability, some or all of the following information may appear:
- Literature Summary: number of references analyzing expression for this gene; links to a table of the ages and assay types analyzed.
- Data Summary - each number links to a summary report:
- Assays - assays analyzing expression of the marker; links to data.
- Results - expression results; links to details.
- Tissues - anatomical structures where expression was analyzed; summary report details whether or not expression was detected.
- Images - images associated with results; summary report displays thumbnails of any associated figures; links to full-size images.
- Theiler stage: List of all developmental stages where expression was analyzed; each summary report lists expression results from that stage.
- Assay Type Results and Assays: assay type used for the analyses; number of results and different assay types link to summary reports (subsets of those described above).
- cDNA source data: number of cDNA clones for this marker; summary report lists clones and tissue sources.
- External Resources: links to expression information for this marker in other than MGI databases.
|
| Other database links |
List of and links to additional external resources with database accession IDs associated to this marker. Examples of these resources are EC, Ensembl Gene Model, DoTS, DFCI,
NIA Mouse Gene Index, Entrez Gene, and dbGSS (for Gene Traps).
|
| Protein domains |
List of InterPro domain IDs and descriptions for protein sequences encoded by the gene. The ID is a link to the InterPro detail page for the domain at the EBI. If there is a SWISS-PROT sequence associated to the marker, you can view the protein domain structure of the SWISS-PROT sequence at InterPro's web site by following the Graphical View of Protein Domain Structure link. |
| Molecular reagents |
Links to summary pages of MGI molecular reagent information for the marker grouped by All nucleic, Genomic, cDNA, Primer pair, Other (i.e., other nucleic acid probes), and Antibody. Note that Genomic, cDNA, Primer pair and Other are subsets of All nucleic. The number in parentheses indicates the total number of items listed in the summary. If you select:
- All nucleic, Genomic, cDNA, Primer pair, Other: link is to Molecular Probes and Clones Query Results -- Summary.
- Antibody: link is to Antibodies Query Results -- Summary.
|
| References |
Some or all of the following, depending on availability:
- Details of one selected reference, linked to its detail page.
- Details of the earliest and latest references, linked to their detail pages.
- All references, linked to a listing on the summary report page. The number in parentheses indicates the total of the references on the summary.
References on the detail and summary pages include a J number (an MGI reference ID) and a short citation, linked to the full citation. |
Other
accession IDs |
List of any other MGI accession IDs associated with this marker. |
The Your Input Welcome button, located at the top right of your screen, appears as part of the detailed query results. Clicking the button brings up a dialogue box for submitting any updates or corrections to the data you are viewing. Our User Support staff will review your comments and make sure the appropriate changes are made. This provides an easy way to help us keep data current.
