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.
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) |
|
|
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 |
|
Alleles and Phenotypes |
|
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 Symbol(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID | MGI Marker Accession ID (comma-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 |
|