MGI Data and Statistical Reports

Downloads of short gene descriptions, gene expression, disease annotations, genetic and molecular interaction, and variant data for mouse available from the Alliance of Genome Resources.

These files, along with some additional reports, are also available from this Index.

Mouse Genetic Markers

1. List of Mouse Genetic Markers (sorted alphabetically by marker symbol, tab-delimited) MGI Marker Accession ID Chromosome cM Position Genome Coordinate Start Genome Coordinate End Genome Strand Marker Symbol Status Marker Name Marker Type Feature Types (|-delimted) Marker Synonyms (|-delimited) Current MGI Accession ID (withdrawn only) Current Marker Symbol (withdrawn only)         MRK_List1.rpt.gz (including withdrawn marker symbols)         MRK_List2.rpt.gz (excluding withdrawn marker symbols)

2. MGI Marker Coordinates (tab-delimited) MGI Marker Accession ID Marker Type Feature Type Marker Symbol Marker Name Chromosome Start Coordinate End Coordinate Strand Genome Build Provider Provider Display         MGI_MRK_Coord.rpt (GRCm39)

Sequence Data

1. MGI Gene Model Coordinates (tab-delimited) MGI Marker Accession ID Marker Type Marker Symbol Marker Name Genome Build Entrez Gene ID NCBI Gene Chromosome NCBI Gene Start NCBI Gene End NCBI Gene Strand Ensembl Gene ID Ensembl Gene Chromosome Ensembl Gene Start Ensembl Gene End Ensembl Gene Strand         MGI_Gene_Model_Coord.rpt (GRCm39)

2. MGI Sequence Coordinates (in GFF format)(tab-delimited) Chromosome Source of Feature Marker Type Start Coordinate End Coordinate Empty Column Strand Empty Column ID=MGI ID;Name=marker symbol;Note=marker feature         MGI_GTGUP.gff (GRCm39)

3. MGI Sequence Coordinates (in GFF3 format)(tab-delimited)         3a.MGI.gff3.gz         3b.MGIreg.gff3.gz (regulatory features)

4. MGI Marker associations to Sequence (GenBank, RefSeq,Ensembl) information (tab-delimited) MGI Marker Accession ID Marker Symbol Status Marker Type Marker Name cM Position Chromosome Genome Coordinate Start Genome Coordinate End Strand GenBank Accession IDs (pipe-delimited) RefSeq Transcript ID (if any) Ensembl Transcript ID (if any) UniProt ID (if any) TrEMBL ID (if any) Ensembl protein ID (if any) RefSeq protein ID (if any) Unigene ID (if any)         MRK_Sequence.rpt

5. MGI Marker associations to SWISS-PROT and TrEMBL protein IDs (tab-delimited) MGI Marker Accession ID Marker Symbol Status Marker Name cM Position Chromosome SWISS-PROT/TrEMBL Protein Accession IDs (space-delimited)         MRK_SwissProt_TrEMBL.rpt

6. MGI Marker associations to SWISS-PROT protein IDs (tab-delimited) MGI Marker Accession ID Marker Symbol Status Marker Name cM Position Chromosome SWISS-PROT Protein Accession IDs (space-delimited)         MRK_SwissProt.rpt

7. MGI Marker associations to Gene Trap IDs (tab-delimited) MGI Marker Accession ID Marker Symbol Status Marker Name cM Position Chromosome Mutant Cell Line IDs (space-delimited)         MRK_GeneTrap.rpt

8. MGI Marker associations to Entrez Gene (tab-delimited) MGI Marker Accession ID Marker Symbol Status Marker Name cM Position Chromosome Type Gene DNA Segment Other Genome Feature Complex/Cluster/Region microRNA Secondary Accession IDs (|-delimited) Entrez Gene ID Synonyms (|-delimited) Feature Types (|-delimited) Genome Coordinate Start Genome Coordinate End Strand BioTypes (|-delimited)         MGI_EntrezGene.rpt

9. MGI Marker associations to Ensembl sequence information (tab-delimited) MGI Marker Accession ID Marker Symbol Marker Name cM Position Chromosome Ensembl Accession ID Ensembl Transcript ID (space-delimited, if any) Ensembl Protein ID (space-delimited, if any) Feature Types (|-delimited) Genome Coordinate Start Genome Coordinate End Strand BioTypes (|-delimited)         MRK_ENSEMBL.rpt

10. MGI Marker associations to Ensembl or NCBI gene models where a gene vs. pseudogene discrepancy exists(tab-delimited) Marker Symbol Provider Source Gene ID Biotype MGI Representative Gene Model         MGI_BioTypeConflict.rpt

11. Primer Sequences Marker Symbol Marker Name Primer Marker Name MGI Marker Accession ID MGI Primer Pair ID Primer 1 Sequence Primer 2 Sequence Amplimer Size Chromosome Map Position         PRB_PrimerSeq.rpt

12. InterPro Domains (tab-delimited) InterPro ID Domain Marker Name MGI Marker Accession ID Marker Symbol         MGI_InterProDomains.rpt

Vertebrate Homology

1. Homology Classes - Includes: mouse, human, rat, zebrafish (tab-delimited) DB Class Key Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM gene ID Genetic Location Genome Coordinates (mouse or human Build) Name Synonyms (pipe-delimited)         HOM_AllOrganism.rpt (sorted by DB Class Key)

2. Human and Mouse Homology Classes with Sequence information (tab-delimited) DB Class Key Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM gene ID Genetic Location Genome Coordinates (mouse or human Build) Nucleotide RefSeq ID (comma-delimited) Protein RefSeq ID (comma-delimited) SWISS-PROT IDs (comma-delimited)         HOM_MouseHumanSequence.rpt (sorted by DB Class Key)

3. Mouse Genes with Alliance Homology and HGNC and CCDS IDs MGI Marker Accession ID Mouse Marker Symbol Mouse Marker Name NCBI Gene ID NCBI Gene Chromosome NCBI Gene start NCBI Gene end NCBI Gene strand Ensembl Gene ID Ensembl Gene chromosome Ensembl Gene start Ensembl Gene end Ensembl Gene strand CCDS IDs (comma delimited) HGNC ID         HGNC_AllianceHomology.rpt

4. Mouse/Human Orthology with Phenotype Annotations (tab-delimited) Human Marker Symbol Human Entrez Gene ID Mouse Marker Symbol MGI Marker Accession ID High-level Mammalian Phenotype ID (comma-delimited)         HMD_HumanPhenotype.rpt

5. Mouse Protein Coding Genes having one-to-one Orthology with Human Genes MGI Marker Accession ID Mouse Gene Symbol Mouse NCBI Gene ID HGNC ID Human Gene Symbol Human NCBI Gene ID         HOM_ProteinCoding.rpt

Gene Ontology Data

1. Marker/SWISS-PROT Associations for Markers with GO Annotations (tab-delimited) MGI Marker Accession ID SWISS-PROT ID (;-delimited)         gp2protein.mgi

2. Gene Ontology (GO) Annotations of Mouse Markers (see also GO Annotation File format at the Gene Ontology Consortium)         Note that GO data in MGI includes recent annotations made after the official release date and thus may not be in the current official release file.         GAF File: https://current.geneontology.org/annotations/mgi.gaf.gz         GPI File: https://current.geneontology.org/annotations/mgi.gpi.gz         GPAD2.0 File: https://current.geneontology.org/annotations/mgi.gpad.gz

Strains and Polymorphisms

1. Official Strain Nomenclature (tab-delimited) MGI Strain ID Strain Name Strain Type         MGI_Strain.rpt         (sorted alphabetically by strain name)

2. Unreviewed Nonstandard Mouse Strain and Stock Nomenclature (tab-delimited) MGI Strain ID Strain Name Strain Type         MGI_Nonstandard_Strain.rpt         (sorted alphabetically by strain name)

3. List of ES Cell Line Names and Strains of Origin (tab-delimited) ES Cell Line Name Strain Name         ES_CellLine.rpt

Gene Expression

1. MGI Genetic Markers with GXD Literature Content Records (tab-delimited) MGI Marker Accession ID Mouse Marker Symbol MGI Reference Accession ID (J:) (comma-delimited)         MRK_GXD.rpt

2. MGI Genetic Markers with GXD Assay Records (tab-delimited) MGI Marker Accession ID Mouse Marker Symbol MGI Assay Accession ID (comma-delimited)         MRK_GXDAssay.rpt

3. RNA-Seq assay results in GXD (tab-delimited file per experiment) MGI Gene ID Ensembl ID Gene Symbol Gene Name Experiment ID Anatomical Structure Theiler Stage Age Sex Strain Mutant Allele Pair(s) Notes Sample ID Number of Biological Replicates Bioreplicate Set Label Detected AVG TPM QN TPM AVG QN TPM          RNA-Seq Report Download Comprehensive reports for each RNA-Seq Experiment in GXD with expression data loaded from the Expression Atlas at EMBL's European Bioinformatics Institute (EBI). Reports include GXD-curated sample metadata and GXD-computed TPM values per gene. GXD imports selected sets of RNA-Seq data from EMBL-EBI's Expression Atlas for experiments that have been annotated to controlled biological source metadata by expert GXD curation. Leveraging curated source metadata, GXD processes the files further to effectively integrate RNA-Seq data with classical expression data in GXD. TPM processing includes several steps. First, we use TPM values in the files imported from the Expression Atlas to compute the average TPM value per gene per sample for technical replicates. Then, we group samples that have the same source information into biological replicate sets and quantile normalize (QN) the TPM values per gene across the samples in each biological replicate set. Finally, to minimize biological sample variation, we average these QN TPM values to arrive at a single TPM value per gene per set of bioreplicate samples. Average QN TPM values are used to assign TPM levels and expression detected/not detected status in the GXD interface. Average QN TPM values are also exported for visualization in Morpheus-derived heat maps of GXD expression results.

4. MGI Microarray Annotation Files (tab-delimited) Probeset ID Sequence ID MGI ID Gene Symbol Gene Name Chromosome Start Coordinate End Coordinate Strand         Affy_1.0_ST_mgi.rpt (Affymetrix Mouse Gene 1.0 ST Array)         Affy_430_2.0_mgi.rpt (Affymetrix GeneChip Mouse Genome 430 2.0 Array)         Affy_U74_mgi.rpt (Affymetrix GeneChip Mouse Genome U74A-B-C_2)

5. Mouse Anatomy in OBO Format         adult_mouse_anatomy.obo

6. Mammalian Phenotype (MP)-Mouse Developmental Anatomy (EMAPA) Mappings MP ID MP Term EMAPA ID EMAPA Term         MP_EMAPA.rpt

Alleles and Phenotypes

1. Mammalian Phenotype Vocabulary in OBO v1.2, tab-delimited, JSON and OWL Formats         MPheno_OBO.ontology         VOC_MammalianPhenotype.rpt         mp.json         mp.owl         mp-international.owl

2. Mouse/Human Orthology with Phenotype Annotations (tab-delimited) Human Marker Symbol Human Entrez Gene ID Mouse Marker Symbol MGI Marker Accession ID High-level Mammalian Phenotype ID (space-delimited)         HMD_HumanPhenotype.rpt

3. List of All Mouse Phenotypic Alleles (tab-delimited) MGI Allele Accession ID Allele Symbol Allele Name Allele Type Allele Attribute PubMed ID for original reference MGI Marker Accession ID Marker Symbol Marker RefSeq ID Marker Ensembl ID High-level Mammalian Phenotype ID (comma-delimited) Synonyms (|-delimited) Marker Name         MGI_PhenotypicAllele.rpt

4. List of All Mouse QTL Alleles (tab-delimited) MGI Allele Accession ID Allele Symbol Allele Name Allele Type PubMed ID for original reference MGI Marker Accession ID Marker Symbol Marker RefSeq ID Marker Ensembl ID Marker Chromosome Marker Start Coordinate Marker End Coordinate Genome Build High-level Mammalian Phenotype ID (comma-delimited)         MGI_QTLAllele.rpt

5. All Genotypes and Mammalian Phenotype Annotations (tab-delimited) Allelic Composition Allele Symbols (pipe-delimited) Genetic Background Mammalian Phenotype ID PubMed IDs (pipe-delimited) MGI Marker Accession IDs (pipe-delimited)         MGI_PhenoGenoMP.rpt

6. List of All KOMP Alleles (tab-delimited) Mutant Cell Line ID Logical DB Name MGI Allele Accession ID Allele Symbol Allele Name MGI Marker Accession ID Marker Symbol         KOMP_Allele.rpt

7. List of All EUCOMM Alleles (tab-delimited) Mutant Cell Line ID Logical DB Name MGI Allele Accession ID Allele Symbol Allele Name MGI Marker Accession ID Marker Symbol         EUCOMM_Allele.rpt

8. List of All NorCOMM Alleles (tab-delimited) Mutant Cell Line ID Logical DB Name MGI Allele Accession ID Allele Symbol Allele Name MGI Marker Accession ID Marker Symbol         NorCOMM_Allele.rpt

9. Genotypes and Mammalian Phenotype Annotations for Marker Type Genes excluding conditional mutations (tab-delimited) Allelic Composition Allele Symbol(s) Allele ID(s) Genetic Background Mammalian Phenotype ID PubMed ID (pipe-delimited) MGI Marker Accession ID (pipe-delimited) MGI Genotype Accession ID (pipe-delimited)         MGI_GenePheno.rpt

10. Genotypes with both Phenotype and Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) Allelic Composition Allele Symbol(s) Allele ID(s) Genetic Background Mammalian Phenotype ID PubMed ID (pipe-delimited) MGI Marker Accession ID (pipe-delimited) DO ID (pipe-delimited) MIM ID (pipe-delimited)         MGI_Geno_DiseaseDO.rpt

11. Genotypes with both Phenotype and Negated Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) Allelic Composition Allele Symbol(s) Allele ID(s) Genetic Background Mammalian Phenotype ID PubMed ID (pipe-delimited) MGI Marker Accession ID (pipe-delimited) DO ID (pipe-delimited) MIM ID (pipe-delimited)         MGI_Geno_NotDiseaseDO.rpt

12. Associations of Mouse Genes with DO Diseases DO Disease ID DO Disease Name OMIM ID (pipe delimited) Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID         MGI_DO.rpt

13. IMSR/KOMP Counts Marker Symbol MGI Marker Accession ID Total number of IMSR Strains Total number of Alleles         MGI_IMSRKomp.rpt

14.Genotypes with Sex-specific Phenotypes Genotype ID Sex MP ID MP Term Allelic Composition Background Strain Sex-specific Normal Y/N Citation (MGI ID if no PubMed ID)         MGI_Pheno_Sex.rpt

15. Mouse models of Human Disease by Human gene (tab-delimited) Human gene symbol Human gene name HGNC id for human gene (pipe-delimited) DO term name associated with human gene DO term ID associated with human gene Mouse genotype IDs associated with DO term (pipe-delimited) Mouse gene Mouse MGI ID Facilities (pipe-delimited) Repository ID (pipe-delimited)         MGI_DiseaseGeneModel.rpt

16. Human Diseases and Mouse Models by Genotype (1:1 orthologs only) (tab-delimited) DO term name associated with human gene DO term ID associated with human gene NOT model Allele Pairs Strain Background Allele symbol Allele MGI ID Total number of allele references Repository ID for allele (pipe-delimited) Mouse genotype RR id (pipe-delimited) Mouse gene symbol Mouse gene ID Repository ID for gene (pipe-delimited)         MGI_DiseaseMouseModel.rpt

Recombinase (cre) Specificity

1. Recombinase (cre) Specificity Driver Allele Symbol Name Detected in Absent in IMSR Strain Allele ID         MGI_Recombinase_Full.html         MGI_Recombinase_Full.rpt (Tab-delimited version)

References

1. Association of MGI Markers and PubMed IDs (tab-delimited) MGI Marker Accession ID Marker Symbol Marker Name Marker Synonyms (|-delimited) PubMed IDs (|-delimited)         MRK_Reference.rpt

2. Association of MGI Reference Accession IDs and PubMed IDs (tab-delimited) MGI Reference Accession ID PubMed ID Alternative MGI Reference Accession ID (J:)         BIB_PubMed.rpt

Clone Collections

1. All Clones (tab-delimited) MGI Clone ID Clone Name MGI Marker ID Marker Symbol Clone Set         MGI_CloneSet.rpt

DNA Mapping Panels

1. Copeland-Jenkins - (C57BL/6J x M.spretus)F1 x C57BL/6J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 205 animals (1 column per animal) J Number         MGI_Copeland-Jenkins_Panel.rpt (tab-delimited)

2. EUCIB (BSB) - (C57BL/6J x SPR or SEG/Pas)F1 x C57BL6J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 482 animals (1 column per animal) J Number         MGI_EUCIB_BSB_Panel.rpt (tab-delimited)

3. EUCIB (BSS) - (C57BL/6J x SPR or SEG/Pas)F1 x SPR or SEG/Pas Chromosome MGI Marker Accession ID Marker Symbol Allele data for 501 animals (1 column per animal) J Number         MGI_EUCIB_BSS_Panel.rpt (tab-delimited)

4. JAX (BSB) - (C57BL/6J x M.spretus)F1 x C57BL/6J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 94 animals (1 column per animal) J Number         MGI_JAX_BSB_Panel.rpt (tab-delimited)

5. JAX (BSS) - (C57BL/6JEi x SPRET/Ei)F1 x SPRET/EiJ Chromosome MGI Marker Accession ID Marker Symbol Allele data for 94 animals (1 column per animal) J Number         MGI_JAX_BSS_Panel.rpt (tab-delimited)

6. JAX Mouse Mutant Resource BCB - (C57BL/6J x CAST/Ei)F1 x C57BL/6J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 144 animals (1 column per animal) J Number         MGI_JAX_Mouse_Mutant_Resource_BCB_Panel.rpt (tab-delimited)

7. JAX Mouse Mutant Resource BSS - (C57BL/6J x SPRET/Ei)F1 x SPRET/EiJ Chromosome MGI Marker Accession ID Marker Symbol Allele data for 139 animals (1 column per animal) J Number         MGI_JAX_Mouse_Mutant_Resource_BSS_Panel.rpt (tab-delimited)

8. Kozak FvC58 - (NFS/N x M.spretus)F1 x C58/J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 93 animals (1 column per animal) J Number         MGI_Kozak_FvC58_Panel.rpt (tab-delimited)

9. Kozak FvSpr - (NFS/N x M.spretus)F1 x M.spretus Chromosome MGI Marker Accession ID Marker Symbol Allele data for 24 animals (1 column per animal) J Number         MGI_Kozak_FvSpr_Panel.rpt (tab-delimited)

10. Kozak Skive - (NFS/N or C58/J x M.m.musculus)F1 x M.m.musculus Chromosome MGI Marker Accession ID Marker Symbol Allele data for 94 animals (1 column per animal) J Number         MGI_Kozak_Skive_Panel.rpt (tab-delimited)

11. MIT - (C57BL/6J-Lep<ob> x CAST)F1 x (C57BL/6J-Lep<ob> x CAST)F1 Chromosome MGI Marker Accession ID Marker Symbol Allele data for 46 animals (1 column per animal) J Number         MGI_MIT_Panel.rpt (tab-delimited)

12. Reeves (Chr 16) - Sex averaged intersubspecific mapping panel Chromosome MGI Marker Accession ID Marker Symbol Allele data for 707 animals (1 column per animal) J Number         MGI_Reeves_Chr_16_Panel.rpt (tab-delimited)

13. Seldin - (C3H/HeJ-Fasl<gld> x M.spretus)F1 x C3H/HeJ-Fasl<gld>/J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 849 animals (1 column per animal) J Number         MGI_Seldin_Panel.rpt (tab-delimited)

14. UCLA (BSB) - (C57BL/6J x M.spretus)F1 x C57BL/6J Chromosome MGI Marker Accession ID Marker Symbol Allele data for 67 animals (1 column per animal) J Number         MGI_UCLA_BSB_Panel.rpt (tab-delimited)