Interpreting a Sequence Summary
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This document answers the following questions about a sequence summary:

See also:

When does a sequence summary appear?

A sequence summary appears:

When you search for sequences... For field details, see...
from a Gene Detail report I clicked a link on a Gene Detail report...
from on a Reference Detail report I clicked a link on a Reference Detail report...

What's in a sequence summary?

The Mouse Sequences Query Results summary appears when you select the All sequences, RefSeq or UniProt links in the Sequences section of a marker detail page. The summary provides a general description of each sequence that your query returns. The summary lists:

You can view MGI sequence details (see Using Sequence Detail Reports), or you can download it in FASTA format or forward it to MouseBLAST.

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How do I use a sequence summary?

There are several ways to use a sequence summary. You can:

  1. view sequence details for a single sequence by clicking either the MGI Sequence Detail or the provider (e.g., GenBank, RefSeq, and so on) link.
  2. download a sequence in FASTA format.
  3. forward a sequence to MouseBLAST.

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How do I view details for a single sequence?

You can elect to view the sequence details in the provider's database or in MGI.

  1. Click the desired provider link (e.g., GenBank |EMBL |DDBJ).
    The provider's sequence record appears.
  2. Click MGI Sequence Detail.
    The detail record for that sequence as stored in MGI appears. See Using Sequence Detail Reports.
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How do I download a sequence in FASTA format?

To download a sequence in FASTA format:

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How do I forward a sequence to MouseBLAST?

To forward a sequence to MouseBLAST:

For additional information, see:

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I clicked a link on a Marker Detail report and got this information. What does it tell me?

You were looking for sequences associated with a gene and clicked All Sequences from the Sequences section of a gene detail report.

Below the header of the Mouse Sequence Summary is the marker symbol, name, and ID, followed by the number of items displayed out of the number found.

The table provides information about the sequences associated with the marker. If a sequence is from the genome assembly, the coordinates appear in the Description from Sequence Provider column.

See What can I do with sequence summary information? for more details.

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I clicked a link on a Reference Detail report and got this information. What does it tell me?

You were looking for sequences associated with a reference and used the Sequences link on a Reference Detail report. The Sequence Summary provides the J number and citation of the reference.

The table provides information about the sequences associated with the reference.

See What can I do with sequence summary information? for more details.

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What can I do with sequence summary information?

On the sequence summary, you can follow links to:

Depending on how you access this summary and your sort choices, some or all of the following fields and links appear:

Select | Sequence | Version | Type | Length | Description from sequence provider | Strain | Tissue | Library | Marker symbol | Marker name | Map position | Genome Coordinates

FieldDescription
SelectCheck boxes for selecting sequences for downloading, or forwarding.
Sequence
  • Sequence identifier
  • Name of the sequence provider, linked to the associated sequence in the provider's database.
  • Link to the MGI sequence detail report
VersionNumber assigned by the provider to this update of the sequence information. If blank, the provider does not furnish this information.
TypeType of sequence: RNA, DNA, or polypeptide.
LengthLength of the sequence, in base pairs (RNA, DNA) or amino acids (polypeptides).
Description from Sequence ProviderInformation about the sequence from the provider you selected (RefSeq, GenBank, and so on.)
Strain/SpeciesMouse strain (or species if other than laboratory mouse) from which the sequence was derived. If the strain/species cannot be resolved to an MGI controlled vocabulary a message to this effect appears, marked with an asterisk. See What does it mean if a value cannot be resolved to an MGI controlled vocabulary?
Source Tissue Mouse tissue from which the sequence was derived.
LibraryMouse library from which the sequence was derived.
Clone CollectionName of clone collections from which the sequence was derived. (Not Applicable appears for RefSeq, UniProt, DFCI, DoTS, NIA sequences)
Marker SymbolGene/marker symbol associated with the sequence(s), linked to the MGI Gene Detail report.
Marker NameName of the gene/marker associated with the sequence.
Map PositionChromosome(s) and cM position(s) of the markers each sequence is associated with.
Genome CoordinatesAssembly sequence coordinates for the mapped gene/marker. Format is Chromosome# (beginning coordinate - end coordinate)

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What does it mean if a value cannot be resolved to an MGI controlled vocabulary?

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 in the MGI databases. 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; a message to this effect, marked with an asterisk, appears on your query report.

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