This help document answers the following questions about using the Accession IDs Query Form:

• What can I use the Accession IDs Query Form to find?
• What do I enter in the Accession IDs Query Form? Can I enter more than one ID? How about a range of IDs?
• What is an MGI accession ID? an external accession ID? a sequence accession ID?
• What happens when I enter a sequence accession ID?
• What is the difference between a primary and a secondary sequence accession ID?
• Can I enter gene trap cell line IDs or IDs associated with cell lines?
• What happens if I enter the accession ID for a clone?
• Which reports can I expect from my query?
• How do I interpret the data in the Accession IDs Query Results -- Summary report?
• Depending on how I query, what can I expect to get back? (examples)
• Can I use any other MGI query forms to find accession IDs?

See also:

• MGI Glossary (unfamiliar terms or acronyms)
• General Guidelines for Searching MGI
• Help Using Wildcards

The system searches the MGI database for any records associated with whatever ID you enter.

What can I use the Accession IDs Query Form to find?

Use the Accession IDs Query Form to find any MGI record that can be identified by an MGI accession ID or an accession ID from an external database (that is, any database cross-referenced in MGI; for example, GenBank). Each MGI record has a permanent MGI Accession ID which identifies it uniquely. Some records also have external database accession IDs stored within them; for example, a gene record typically has several GenBank accession IDs of sequences related to the gene. See also Depending on how I query, what can I expect to get back?.

MGI database records include genes, genetic markers, gene traps, clones, probes, homology, sequences, alleles, assays, human diseases, and references.

MGI Accession IDs (MGI:####) include:

• Mouse Gene/Marker Accession ID
• Reference Accession ID
• Experiment Accession ID
• Probe Accession ID

External databases include:

• Genes and Markers
  • BROAD (Whitehead Institute/MIT Center for Genome Research)
  • DoTS (EPConDB)
  • E.C. Number ENZYME - Enzyme nomenclature database)
  • Ensembl (Mouse Genome Browser and Gene Model)
  • Entrez
  • NIA Mouse Gene Index (National Institute on Aging at NIH)
  • DFCI Gene Indices (The Gene Index Project at the Dana Farber Cancer Institute)
  • UniGene at NCBI
  • Gene Ontology (GO) *
• Sequences
  • BROAD (Whitehead Institute/MIT Center for Genome Research)
  • dbGSS GenBank's Genome Survey Sequences (GSS) division at NCBI
  • DoTS (EPConDB)
  • Ensembl (Mouse Genome Browser and Gene Model)
  • GenBank/EMBL/DDBJ at NCBI
  • RefSeq (NCBI Reference Sequences)
  • NIA Mouse Gene Index (National Institute on Aging at NIH)
  • SWISS-PROT at UniProt
  • DFCI Mouse Gene Index Dana Farber Cancer Institute - The Gene Index Project
  • TrEMBL at UniProt
  • UniGene at NCBI
  • Vega Mouse (Vertebrate Genome Annotation mouse gene model) at Sanger Institute
• Protein Domains
  • InterPro
• Protein Structures
• PDB (Protein Data Bank)
• Protein Superfamilies
  • PIRSF (Protein Information Resource Superfamilies)
• Orthology Relationships
• E. C. (Enzyme Commission)
• HGNC (HUGO Gene Nomenclature Committee)
• Homologene at NCBI
• TreeFam (phylogenetic trees of animal genes)
• References
• Entrez at NCBI
• Pubmed at NCBI
• Probes/Clones
• Affymetrix
• ATCC (American Type Culture Collection)
• BROAD (Whitehead Institute/MIT Center for Genome Research)
• GenBank/EMBL/DDBJ at NCBI
• IMAGE (Integrated Molecular Analysis of Genomes and their Expression)
• MGC (Mammalian Gene Collection)
• RIKEN
• RPCI - 23 Female (C57BL/6J) Mouse BAC Library
• RPCI - 24 Male (C57BL/6J) Mouse BAC Library
• UniSTS (at NCBI)
• Human Diseases
• OMIM at NCBI
• SNPs
• dbSNP at
• NCBI
• Gene Traps
• dbGSS at
• NCBI

* MGI staff curate the Gene Ontology (GO) and the annotation of GO terms to MGI gene records.

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What do I enter in the Accession IDs query form? Can I enter more than one ID? How about a range of IDs?

The form has a single field for entering the Accession ID(s).

• Enter one or more Accession IDs from MGI or any of the external databases associated to MGI database records. (See Depending on how I query, what can I expect to get back? (examples) for additional details.) Place a comma after each entry (except the final one).
• Click Search to submit the query. Click Reset to clear the fields and return any default values.
• See the table below for syntax options.

To find...	Do this...	Examples
Records associated with a specific Accession ID	Enter the complete Accession ID. Be sure to include prefixes where necessary.	MGI:87895
Multiple records from MGI and/or external database(s)	Enter the complete Accession IDs, separated by commas (with or without a space next).	J:14135,MGI:15219,GO:0005892,168600 or J:14135, MGI:15219, GO:0005892, 168600
Multiple records from the same database	If the ID contains a prefix, use a single, initial to enter multiple IDs. Connect them using the plus sign (+).	MGI:15219+30152+6338 GO:0004016+0005886+0006171
Records associated with a specified range of Accession IDs	Enter the first member of the range followed by two dots (..) and the last item in the range. NOTE: Only the initial prefix (if the ID contains one) is necessary. Do NOT include a prefix in the last item.	To see J numbers 8485 through 8590, enter J:8485..8590.

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What is an MGI accession ID? an external accession ID? a sequence accession ID?

MGI accession IDs

• Every MGI database record has an Accession ID of the form MGI:nnnn with the exception of sequences, which use the provider's accession ID.
• In earlier releases, MGI records had accession IDs of varying formats. Older format IDs are sometimes referred to in published papers, so MGI retains these numbers. You can still search for records using the older format accession IDs.
• Every reference stored in MGI has a J number of the form J:nnnn.
• An MGI record may be associated with multiple accession IDs.

The following table describes various MGI database accession IDs.

Accession ID	Format	MGI Data Set
MGI Accession ID	MGI:####...(1-up)	Current accession ID format for references, markers, sequences, experiments and molecular probes/clones, assays, antibodies, antigens, or images (related to gene expression assays)
J number	J:#### (1 - up)	MGI accession ID format for references
MGD Experiment Accession ID	MGD-CREX-#### MGD-RIEX-#### MGD-INEX-#### MGD-HYEX-#### MGD-FIEX-#### MGD-TEXT-####	Older format MGD experiment accession IDs for mapping experiments
MGD Marker Accession ID	MGD-MRK-####	Older format MGD marker accession IDs

External database accession IDs

External database accession IDs are stored in MGI and are also associated with MGI records. For example, a reference record may include a PubMed ID; a molecular probe record may include a GenBank ID. If you search MGI using an external database accession ID, the system returns any MGI records that include this accession ID. See External Databases for a list.

Sequence Accession IDs

Sequence accession IDs are assigned by each sequence provider. Searching for sequences in the MGI database is via the provider's accession ID rather than by an MGI accession ID. See What happens when I enter a sequence accession ID?

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What is the difference between a primary and a secondary sequence accession ID?

Sequences normally have only one primary sequence identifier. Sometimes a sequence record from a provider contains other identifiers, called secondary seqIDs, which also identify this record and possibly other sequence records. On MGI reports, primary sequence identifiers appear in bold font style and secondary seqIDs appear in plain font style.

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What happens when I enter a sequence accession ID?

If the MGI database contains the sequence record, querying by sequence accession ID returns links to all associated MGI sequence, marker, and probe/clone detail reports. If there are no associations to the sequence, the MGI Sequence Detail report appears. This sequence can be from mouse, human, or rat.

If you enter a secondary accession ID, that ID may be associated with more than one sequence.

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Can I enter gene trap cell line IDs or IDs associated with cell lines?

Yes. You can search by for gene traps by cell line ID, sequence tag ID, or GenBank IDs (from dbGSS) associated with the sequences.

• All cell lines are gene traps.
• Gene trap cell line IDs and gene trap sequence tag IDs are assigned by the provider.
• Sequence tag IDs are generated from existing cell line IDs.
• There maybe be many sequence IDs associated with a given cell line ID, but all sequences should be related to a single allele.
• Depending on the technique used and the amount of time spent sequencing, there can be DNA, RNA, forward, and reverse sequence tag ID.
• Each cell line sequence tag also has a GenBank (dbGSS) sequence ID.

See Who are the cell line creators? for examples.

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What happens if I enter a gene trap cell line ID or a gene trap sequence ID?

If the gene trap cell line ID that you enter is:

• associated with a marker, the Accession ID summary report returns two records:
  1. one for the marker associated with the ID, with a link to the marker's gene detail page
  2. one for the allele associated with the ID, with a link to the gene trapped allele detail page.


• not associated with a marker, the summary report returns two records:
  1. one for the allele associated with the gene trap cell line ID, with a link to its allele detail page
  2. one for the sequence tag associated with the gene trap cell line ID, with a link to its sequence detail page.

A gene trap cell line is not associated with a marker if:

• it is mixed (that is, it contains more than one likely gene trap insertion, as determined by sequence tags from separate chromosomes or at a greater distance from one another than would be covered by a single gene)
• any associated sequence tags map to a location containing no known genes.
• any associated sequences map to a location containing multiple genes.
• any associated sequences map in the reverse orientation to a known marker.

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What happens if I enter the accession ID for a clone?

When you type in an accession ID, the query returns links to reports of sequences associated with molecular segment records that in turn are associated with that clone's accession ID. If the clone accession ID is associated to other objects (molecular probes and segments), links to these detail reports appear as well, grouped by sequences and molecular probes/segments.

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Which reports can I expect from my query?

• If your search yields only one record, the system returns that detail report.
• If the search yields more than one record, the system returns a summary report section. Click the desired item to see its detail report.
• If you search using an accession ID from an external database and get zero (0) results, it means that, at this time, MGI has no records containing that accession ID.

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How do I interpret the data in the Accession IDs Query Summary report?

When there is more than one result, the Accession IDs Query Results--Summary report displays all the MGI record types associated with the accession IDs you entered on the query form. Accession IDs are associated with MGI database records for genes, genetic markers, clones, probes, homology, sequences, alleles, gene traps, assays, human disease, and references.

FIELD	DESCRIPTION
AccID	Accession identifier for the query.
Database	Name of the database associated with the AccID, linked to that database's record for the AccID. For MGI accession IDs, the link is in the next column to the right.
MGI Links	Name of and link to the MGI report for the record retrieved (e.g., Allele, Assay, Human Disease, Marker, Probe, Protein Superfamily, Orthology, Reference, Sequence). Note: Although the search may find matches on accession identifiers for human or rat genes and display them in the AccID column, the MGI Links column remains empty when there are no MGI orthologs for those genes.
Type	Kind of record retrieved. Examples: marker (gene, QTL, cytogenetic marker), GO term (biological process, molecular function, cellular component), DNA segment(clone, probe, primer), homology/orthology, experiment, expression assay type (immunohistochemistry, in situ, sequence (RNA, DNA, polypeptide), SNP, and so on.
Description	If ID is from assembly sequence (e.g. Ensembl, NCBI, Vega gene model), ID and genome coordinates appear. If a marker (or probe) is associated with sequence, marker name and/or short citation and/or definition appear. Otherwise, this column briefly describes the MGI detail report for the record. If organism is not mouse, species appears in parentheses at end; e.g., Perc64, PE responsive protein c64, Chr UN (Rat).

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Depending on how I query, what can I expect to get back? (examples)

Note: The examples below are representative of accession IDs in the database, but on any given day, querying the example ID may not yield a result, due to the timing of our curation and data loads.

If you query by...	The result is...	For example...	The format is...
Expression
MGI assay ID	Expression	MGI:1339505	Alphanumeric with colon
Genes and Markers
MGI Marker ID	MGI records containing a list of markers or, if there is a single marker associated with the ID, the detail report for that marker.	MGI:87895, MGD-MRK-1672	Alphanumeric with colon
BROAD		D1184	Alphanumeric
dbGSS mutant cell line ID		FHCRC-GT-S15-11C1	Alphanumeric
DFCI Mouse Gene Index ID		TC1572427	Alphanumeric
DoTS ID		DT.529646	Alphanumeric with decimal
E.C. number		2.7.1.112	Numeric with decimals
Ensembl ID		ENSMUSG00000005672	Alphanumeric
Entrez ID		16590	Numeric
NIA Mouse Gene Index ID		U041021	Alphanumeric
TreeFam ID		TF3201465	Alphanumeric
UniGene ID		4394	Numeric
UniProt		P6281	Alphanumeric
UniSTS		125993	Numeric
VEGA ID		OTTMUSG00000010935	Alphanumeric
Gene Classifications
Gene Ontology (GO) ID	Markers	GO:00302641	Alphanumeric with colon
Human Diseases
OMIM	MGI human disease and mouse model detail reports	168600	Numeric
Orthology Relationships
E.C. Number	Orthology	2.7.1.112	Numeric with decimals
Ensembl ID		ENSMUSG00000005672	Alphanumeric
Entrez Gene ID		56063	Numeric
Homologene		20151	Numeric
HGNC ID		HGNC:28837	Alphanumeric with colon
RefSeq ID		NM_09118	Alphanumeric with underscore
VEGA ID		OTTMUSG00000010935	Alphanumeric
Probes/Clones
Affymetrix tissue/probe ID	Probes/Clones and Sequences	10379153 1424714_at 1451461_a_at	Numeric or alphanumeric with underscore(s)
ATCC clone ID		719230	Numeric
BROAD		D1184	Alphanumeric
GenBank/EMBL/DDBJ ID		AA212080	Alphanumeric
IMAGE clone ID		MGI:200469	Alphanumeric with colon
MGC		14049	Numeric
RIKEN clone ID		MGI:2420147	Alphanumeric with colon
RPCI	RP23-100A23	Alphanumeric
Protein Domains
InterPro ID	Markers	IPR003599	Alphanumeric
InterPro ID	Markers	IPR003599	Alphanumeric
Protein Structures
PDB ID	Markers	1FRB	Alphanumeric
Protein Superfamilies
PIRSF ID	Markers and Sequences	PIRSF018961	Alphanumeric
References
PubMed ID	References	M14791, 8825637	Alphanumeric or numeric
PubMed ID		99236653	Numeric
MGI reference ID		MGI:15219	Alphanumeric with colon
J number		J:14135	Alphanumeric with colon
SNPs
dbSNP	RefSNPs and assay IDs	rs3021544 ss12750703	Alphanumeric
Sequences
GenBank/EMBL/DDBJ ID	Markers, Probes/Clones, Sequences	S40294	Alphanumeric
RefSeq ID	Markers and sequences	NM_0211099	Alphanumeric with underscore
Ensembl ID		ENSMUSG00000005672	Alphanumeric
SWISS-PROT ID		P05532	Alphanumeric
TrEMBL ID		AAA37420	Alphanumeric
DFCI Mouse Gene Index ID		TC1572427	Alphanumeric
DoTS ID		DT.529646	Alphanumeric with decimal
NIA Mouse Gene Index ID		U041021	Alphanumeric with dash
UniGene ID		4394	Numeric
UniSTS		125993	Numeric
VEGA ID		OTTMUSG00000015949	Alphanumeric
Gene trap IDs			Alphanumeric, some with special characters (e.g., dash or underscore)
See Cell Line Creators and Accession IDs for specific examples.

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Can I use any other MGI query forms to find accession IDs?

Several MGI query forms provide options to search for accession IDs associated with specific kinds of records. You can enter one or more accession IDs either from MGI or from any of the external databases that are associated to MGI database records. For example:

Query Form	Source Field	Enter in the Query Form...
References	Reference Accession ID	J number, PubMed ID, or MGI accession ID for the reference.
Genes and Markers	Accession ID	MGI accession ID or external accession IDs including GenBank ID, UniPROT accession ID, older format MGD accession ID (MGD-MRK-####), or Enzyme Commission (EC) number
Mapping Data	Experiment Accession ID	MGI Accession IDs of the form MGI:#### are assigned to all experiment records submitted as of May 1997. Older format MGD accession IDs are retained, and you can use them for searching.
Mammalian Orthology	Reference Accession ID, Marker Accession ID	Unique ID assigned to the article referenced in MGI. Search by MGI Accession ID, J number, or PubMed ID. Enter a single ID, multiple IDs separated by commas, or a range of IDs. When you use the Reference Accession ID field, the system searches for all orthology records associated with the article referenced.
Molecular Probes	Probe Accession ID	MGI Accession ID (the unique ID assigned a probe/clone record in MGI), GenBank ID, IMAGE ID, ATCC ID, WashU ID, RIKEN clone ID, MGC ID, etc.
cDNA Clone	Probe Accession ID	MGI Accession ID (the unique ID assigned a probe/clone record in MGI), GenBank ID, IMAGE ID, ATCC ID, WashU ID, RIKEN clone ID, etc.

You can use the All Search Tools menu to locate the other MGI query forms.

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