Interpreting a Sequence Summary
Interpreting a Sequence Summary
This document answers the following questions about a sequence summary:
See also:
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...
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 NCBI BLAST.
There are several ways to use a sequence summary. You can:
You can elect to view the sequence details in the provider's database or in MGI.
To download a sequence in FASTA format:
To forward a sequence to NCBI BLAST:
For additional information, see NCBI BLAST Help for how to use this tool.
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.
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.
On the sequence summary, you can follow links to:
| Select | Sequence | Type | Length | Strain | Description From Sequence Provider | Clone Collection | Marker symbol |
| Field | Description |
|---|---|
| Select | Click the appropriate link to download the sequence in FASTA format or to forward it to NCBI BLAST. |
| Sequence |
|
| Version | Number assigned by the provider to this update of the sequence information. If blank, the provider does not furnish this information. |
| Type | Type of sequence: RNA, DNA, or polypeptide. |
| Length | Length of the sequence, in base pairs (RNA, DNA) or amino acids (polypeptides). |
| Strain/Species | Mouse 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? |
| Description from Sequence Provider | Information about the sequence from the provider you selected (RefSeq, GenBank, and so on.) |
| Clone Collection | Name of clone collections from which the sequence was derived. (Not Applicable appears for RefSeq, UniProt, DFCI, DoTS, NIA sequences) |
| Marker Symbol | Gene/marker symbol associated with the sequence(s), linked to the MGI Gene Detail report. |
| Marker Name | Name of the gene/marker associated with the sequence. |
| Map Position | Chromosome(s) and cM position(s) of the markers each sequence is associated with. |
| Genome Coordinates | Assembly sequence coordinates for the mapped gene/marker. Format is Chromosome# (beginning coordinate - end coordinate) |
You can filter results by Strain and sequence Type. Click a "Filter sequences by" button above your results and check the items you wish to retain after filtering.
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.