Interpreting Gene Details
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This help document answers the following questions about the Gene Detail Report.

What determines the title of this report?

The title of this report describes the marker and genomic feature type returned as a result of your query. The title may identify a gene, segment, pseudogene, marker, BAC/YAC end, complex/cluster/region, or some other genome feature including "Miscellaneous Genome Feature Detail."

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Which fields should show up on this report?

Depending on data availability and the marker type, this detail report contains information in some or all of the following categories:

Symbol/Name/ID | Synonyms | STS | Feature Type | Genetic Map | Sequence Map | Vertebrate homology | Human homologs | Alleles & Phenotypes | Interactions | Gene Ontology (GO) Classifications | Expression | Molecular reagents | Other database links | Sequences | Polymorphisms | Protein-related information | References | Other accession IDs
Field Description
SymbolOfficial gene symbol for the mouse genetic marker. 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.
NameThe name for this marker appears beneath the symbol.
IDThe MGI accession identifier appears beneath the name.
Cluster members/
Member of
For complex/cluster/region feature types, this section may provide links to up to three of the cluster member detail pages, along with a link to a list of all the cluster members. A pop-up window generated by selecting the link offers the option of getting "More data for these features" by forwarding the list to the MGI Batch Query. For markers that are members of a cluster, a link is provided to the cluster detail page. MGI defines a cluster as a group of closely linked genes that are related by evolution or function.
 

BioType Conflict

  • When different annotation groups disagree as to the marker type (e.g., protein coding versus pseudogene), click Biotype Conflict to see details about the conflict.
  • Identifiers in the Gene ID column link to the database source of the annotation(i.e., VEGA, Ensembl, NCBI).

Strain-Specific Marker

  • When a marker is strain specific and strain data is known, click Strain-Specific Marker for details such as the presence/absence of this gene in a given strain or notes about this genomic region appear.
  • If there are strain-specific references, they appear at the bottom of this box, linked to the MGI Reference Detail Page.

Synonyms Names or symbols for a given marker that may appear in the literature but which are not approved names or symbols.
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.
Feature TypeGenetic feature type(s) annotated to the marker (e.g, snoRNA gene, rRNA gene and so on). See Genome Feature Type Definitions for a complete list of Feature Types used in MGI and their definitions.
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).
  • Marker's centimorgan position. Centimorgan positions for genes and markers in MGI are based on linear interpolation using the standard genetic map described in Cox et al. (2009) (PMID). Markers without genome coordinates cannot be assigned specific cM locations and are designated as syntenic.
  • Cytogenetic position.
Sequence MapAppears if coordinates are assigned and includes:
  • genome coordinate range and strand, in base pairs (provider of genomic coordinates is indicated)
  • a Get FASTA button will download the genomic sequence based on the coordinates. You can also add an equal amount of flanking sequence to each end.
  • 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.
Vertebrate
homology
Vertebrate homology records for this marker, as follows (depending on availability):
  • The HomoloGene ID for this genomic feature and a link to the MGI Vertebrate Homology Class page of homology relationships
  • A list of species with curated homology relationships and the number of related markers for each species
  • 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
  • A link to the Gene Tree View at Ensembl (phylogenetic trees of animal genes).
Human
homologs
Human homolog records for this marker, if available, as follows:
  • Official human gene symbol, name and NCBI Gene ID
  • A link to human protein data at neXtProt
  • Human Synonyms: Names or symbols for a given marker that may appear in the literature but which are not approved names or symbols
  • Human chromosome, cytogenetic band position, and genome coordinate range and strand, in base pairs, from NCBI
  • The number of human diseases associated with this gene in OMIM. When you click on this number a pop-up window appears listing the associated diseases (linked to the MGI Human Disease and Mouse Model Detail page) and the OMIM ID (linked to the OMIM entry for that disease). An asterisk appears if a mouse model of that disease is associated with mutations in the orthologous mouse gene. Note: Inclusion in this report does not necessarily mean that mutations in the gene of interest contribute to or cause the disease listed in the Human Disease column. The gene may have an allele that is part of a complex genotype that includes other causative genes.
Mutations, alleles, and phenotypes Depending on availability, the display includes some or all of the following links or information. The numbers in parentheses indicate how many items in each linked report.
  • Counts of All mutations/alleles and phenotypic allele categories of mutant alleles
  • A short summary of phenotypes observed in mice with mutant alleles
  • Incidental mutations with links to data from the mutagenesis projects. Incidental mutations have been detected via sequencing but have not yet been confirmed. They may or may not affect the phenotype. Click on one of the project links, such as Mutagenetix or APF (The Australian Phenomic Facility), to access the provider's data. Stocks can be ordered from the providers. See Selecting Phenotypic Allele Categories for a list of mutagenesis projects.
  • The number of human diseases associated with this mouse gene in MGI. When you click on this number a pop-up window appears listing the associated diseases (linked to the MGI Human Disease and Mouse Model Detail page) and the OMIM ID (linked to the OMIM entry for that disease).
  • Alleles Annotated to Human Diseases: links to the Phenotypic Alleles Query Results -- Summary page for alleles with OMIM annotations to associated genotypes
  • Phenotype Images: links to the All Phenotype Images for Gene report with every phenotype image in MGI for the gene.

InteractionsThe total number of markers with which the gene is known or suspected of interacting, along with links to up to three of those markers' detail pages and a link to View All the markers. See Interpreting Interaction Explorer Results for more information on MGI interaction data.
Gene Ontology (GO)
Classifications
  • All GO classifications (# annotations) links to a summary of the nn annotated items found (click here for information about interpreting the fields on this page). You can browse the GO vocabulary from the query results section and locate multiple terms that annotate a gene record.
  • Links to GO annotations for Process (biological), Component (cellular), and Function (molecular) of the gene
  • A link to the GO Consortium Reference Genome Annotation Project, if this gene is annotated in the project
  • A link to any External Resources (for example, FuncBase, a database of functional predictions) for additional information about this gene.
Expression The Gene Expression Database (GXD) logo appears in the left hand column. Click on the logo for more information on GXD and its tools.

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:
    • 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
    • Tissue x Stage Matrix - displays a grid of the developmental stages/ages for the tissues assayed for this gene.
  • Assay Type Results: assay type used for the analyses and the number of results, linked to summary reports.
  • cDNA source data: the number of cDNA clones for this marker, linked to summary report.
  • External Resources: links to expression information for this marker in other than MGI databases. Examples: Allen Brain Atlas, GENSAT, gene microarray profile pages at GEO, Expression Atlas.
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 Microarray probesets. 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.
  • Microarray probeset: link is to Microarray Probeset Summary.
Other database links
  • List of and links to external resources with database accession IDs associated to this marker. Examples are EC, Ensembl Gene Model, DoTS, DFCI, NIA Mouse Gene Index, Entrez Gene, International Mouse Knockout Project Consortium Status.
  • Additionally, there may be links to the sequence evidence underlying gene predictions provided by NCBI, Ensembl, and VEGA.
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 representative 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. If a marker is associated with RefSeq and/or UniProt sequences, the numbers of such associations appear, linked to separate Mouse Sequence Summary Reports for all sequences of those types.

Note on representative sequence display:
MGI Representative Sequences provide users quick access to a single genomic, transcript and polypeptide sequence (where available) for the featured gene. To view all sequences for the gene, follow the All sequences link at the bottom of the Sequences section.
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.
Protein-related information
  • List of InterPro domain IDs & descriptions for protein sequences encoded by the gene. The ID links to the InterPro detail page for the domain at the EBI. If there is a SWISS-PROT sequence associated to the marker, click Graphical View of Protein Domain Structure to view the protein domain structure of the SWISS-PROT sequence at InterPro web.
  • Links to Protein Ontology for those genes with mappings to PRO IDs.
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.
  • Disease annotation references, linked to a listing of just those references with human disease model annotations. The number in parentheses indicates the number of these 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.

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How can I tell which dbSNP build this data is from?

The dbSNP build number appears (in parentheses) in the Polymorphisms column, in the middle of the report.
Example:   All PCR and RFLP(28) : PCR(3) RFLP(25) SNPs within 2kb (622 from dbSNP Build 128)

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What happens if I click Your Input Welcome?

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.

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