| Sequence Data |
|---|
| 1. MGI Sequence Coordinates (tab-delimited) |
| MGI Marker Accession ID |
Marker Type |
Marker Symbol |
Marker Name |
Representative Genome ID |
Representative Genome Chromosome |
Representative Genome Start |
Representative Genome End |
Representative Genome Strand |
Representative 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 |
VEGA Gene ID |
VEGA Gene Chromosome |
VEGA Gene Start |
VEGA Gene End |
VEGA Gene Strand |
UniSTS Gene Chromosome |
UniSTS Gene Start |
UniSTS Gene End |
MGI QTL Gene Chromosome |
MGI QTL Gene Start |
MGI QTL Gene End |
miRBase Gene ID |
miRBase Gene Chromosome |
miRBase Gene Start |
miRBase Gene End |
miRBase Gene Strand |
Roopenian Gene Start |
Roopenian Gene End |
|
| MGI_Coordinate.rpt (Build 37) |
|
| 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 (Build 37) |
|
| 3. MGI Marker associations to Sequence (GenBank, RefSeq,VEGA, Ensembl) information (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | Status | Marker Type | Marker Name | cM Position | Chromosome |
GenBank Accession IDs
(space-delimited) | Unigene ID
(if any) | RefSeq ID
(if any) | VEGA Transcript ID
(if any) | Ensembl Transcript ID
(if any) |
|
| MRK_Sequence.rpt |
|
| 4. 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 |
|
| 5. 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 |
|
| 6. 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 |
|
7. 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) | BioTypes
(|-delimited) | Feature Types
(|-delimited) |
|
| MGI_EntrezGene.rpt |
|
| 8. MGI Marker associations to VEGA sequence information (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | Marker Name | cM Position | Chromosome |
VEGA Accession ID | VEGA Transcript ID
(space-delimited, if any) | VEGA Protein ID
(space-delimited, if any) |
|
| MRK_VEGA.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) |
|
| MRK_ENSEMBL.rpt |
|
| 10. MGI Marker associations to VEGA, 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. MGI Marker associations to InterPro IDs (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | InterPro Accession IDs (space-delimited) |
|
| MRK_InterPro.rpt |
|
|
| 14. MGI Marker associations to RIKEN Clones (tab-delimited) |
| RIKEN Clone ID | MGI Clone ID | GenBank Sequence ID | Problem Sequence? | MGI Marker Accession ID | Marker Symbol | Marker Name |
|
| MGI_RIKEN.rpt |
|
| 15. MGI Marker associations to All Sequences and Human Orthology (tab-delimited) |
| MGI Marker Accession ID |
Mouse Symbol |
Mouse Name |
cM Position |
Mouse 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 |
VEGA Gene ID |
VEGA Gene Chromosome |
VEGA Gene Start |
VEGA Gene End |
VEGA Gene Strand |
GenBank IDs
(comma-delimited) |
Unigene IDs
(comma-delimited) |
RefSeq IDs
(comma-delimited) |
Ensembl Transcript IDs
(comma-delimited) |
Ensembl Protein IDs
(comma-delimited) |
VEGA Transcript IDs
(comma-delimited) |
VEGA Protein IDs
(comma-delimited) |
SwissProt IDs
(comma-delimited) |
InterPro IDs
(comma-delimited) |
Mouse Synonyms
(comma-delimited) |
Human Entrez Gene ID |
Human Symbol |
Human Name |
Human Chr |
Human RefSeq IDs
(comma-delimited) |
Human Synonyms
(comma-delimited) |
|
| MGI_MouseHumanSequence.rpt (Build 37) |
|
|
|
| Mammalian Orthology |
|---|
| 1. Human and Mouse Orthology |
| Human Chromosome | Human Entrez Gene ID | Human Marker Symbol | Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position |
Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Human1.rpt (sorted by human chromosome, space-delimited) |
| HMD_Human5.rpt (sorted by human chromosome, tab-delimited) |
|
| 2. Human and Mouse Orthology |
| Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position | Mouse Entrez Gene ID | Mouse Marker Symbol | Human Chromosome |
Human Entrez Gene ID | Human Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Human2.rpt (sorted by mouse chromosome) |
|
| 3. Human and Mouse Orthology |
| Human Entrez Gene ID | Human Marker Symbol | Human Chromosome | Mouse MGI Accession ID | Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Chromosome |
Mouse cM Position | Mouse Cytogenetic Band | Data Attributes |
|
| HMD_Human3.rpt (sorted by human marker symbol) |
|
| 4. Human and Mouse Orthology |
| Mouse MGI Accession ID | Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Chromosome | Mouse cM Position | Mouse Cytogenetic Band |
Human Entrez Gene ID | Human Marker Symbol | Human Chromosome | Data Attributes |
|
| HMD_Human4.rpt (sorted by mouse marker symbol) |
|
| 5. Human and Mouse Orthology (HGNC) (tab-delimited) |
| MGI Marker Accession ID | Mouse Marker Symbol | Mouse Marker Name | Mouse Entrez Gene ID | HGNC ID | HGNC Human Marker Symbol | Human Entrez Gene ID |
|
| HMD_HGNC_Accession.rpt |
|
6. Human and Mouse Orthology with Sequence information (tab-delimited)
| Mouse Marker Symbol |
MGI Marker Accession ID |
Mouse Entrez Gene ID |
Human Marker Symbol |
Human Entrez Gene ID |
Mouse Nucleotide RefSeq ID (comma-delimited) |
Human Nucleotide RefSeq ID (comma-delimited) |
Mouse Protein RefSeq ID (comma-delimited) |
Human Protein RefSeq ID (comma-delimited) |
Mouse SWISS-PROT IDs
(if any, comma-delimited) |
Human SWISS-PROT ID
(if any, comma-delimited) |
Mouse GenBank Accession IDs
(if no RefSeq or SWISS-PROT, comma-delimited) |
Evidences used to support the mouse-human orthology
(comma-delimited) |
J Numbers for references supporting the orthology (comma-delimited) |
PubMed IDs for references supporting the orthology (comma-delimited) |
|
| HMD_HumanSequence.rpt |
|
| 7. Human and Mouse Orthology with Human OMIM Gene IDs |
| MGI Marker Accession ID | Mouse Marker Symbol | Human Marker Symbol | OMIM Gene ID |
|
| HMD_OMIM.rpt |
|
| 8. Human and Mouse Orthology with Synonyms (tab-delimited) |
| Mouse MGI Accession ID | Mouse Marker Symbol | Mouse Entrez Gene ID | Human Entrez Gene ID | Mouse Marker Synonym | Human Marker Symbol |
|
| HMD_Synonyms.rpt |
|
| 9. Rat and Mouse Orthology |
| Rat Chromosome | Rat Entrez Gene ID | Rat Marker Symbol | Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position |
Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Rat1.rpt (sorted by rat chromosome, space-delimited) |
| HMD_Rat5.rpt (sorted by rat chromosome, tab-delimited) |
|
| 10. Rat and Mouse Orthology |
| Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position | Mouse Entrez Gene ID | Mouse Marker Symbol | Rat Chromosome |
Rat Entrez Gene ID | Rat Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Rat2.rpt (sorted by mouse chromosome) |
|
| 11. Rat and Mouse Orthology |
| Rat Entrez Gene ID | Rat Marker Symbol | Rat Chromosome | Mouse MGI Accession ID | Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Chromosome |
Mouse cM Position | Mouse Cytogenetic Band | Data Attributes |
|
| HMD_Rat3.rpt (sorted by rat marker symbol) |
|
| 12. Rat and Mouse Orthology |
| Mouse MGI Accession ID | Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Chromosome | Mouse cM Position | Mouse Cytogenetic Band |
Rat Entrez Gene ID | Rat Marker Symbol | Rat Chromosome | Data Attributes |
|
| HMD_Rat4.rpt (sorted by mouse marker symbol) |
|
| 13. Rat and Human Orthology |
| Rat Chromosome | Rat Entrez Gene ID | Rat Marker Symbol | Human Chromosome |
Human Entrez Gene ID | Human Marker Symbol | Data Attributes |
|
| HMD_RatHuman1.rpt (sorted by rat chromosome, space-delimited) |
| HMD_RatHuman5.rpt (sorted by rat chromosome, tab-delimited) |
|
| 14. Rat and Human Orthology |
| Human Chromosome | Human Entrez Gene ID | Human Marker Symbol | Rat Chromosome |
Rat Entrez Gene ID | Rat Marker Symbol | Data Attributes |
|
| HMD_RatHuman2.rpt (sorted by human chromosome) |
|
| 15. Rat and Human Orthology |
| Rat Entrez Gene ID | Rat Marker Symbol | Rat Chromosome | Human Entrez Gene ID | Human Marker Symbol | Human Chromosome | Data Attributes |
|
| HMD_RatHuman3.rpt (sorted by rat marker symbol) |
|
| 16. Rat and Human Orthology |
| Human Entrez Gene ID | Human Marker Symbol | Human Chromosome |
Rat Entrez Gene ID | Rat Marker Symbol | Rat Chromosome | Data Attributes |
|
| HMD_RatHuman4.rpt (sorted by human marker symbol) |
|
| 17. Mouse/Human/Rat Oxford Grid Counts (tab-delimited) |
| Species 1 | Species 2 | Species 1 Chromosome | Species 2 Chromosome | Number of Orthologies |
|
| HMD_OxfordGrid.rpt |
|
| 18. Mouse/Human Orthology with Phenotype Annotations (tab-delimited) |
| Human Marker Symbol | Human Entrez Gene ID | Mouse Marker Symbol | MGI Marker Accession ID | Mammalian Phenotype ID
(space-delimited) |
|
| HMD_HumanPhenotype.rpt |
|
| 19. Chimpanzee and Mouse Orthology |
| Chimpanzee Chromosome | Chimpanzee Entrez Gene ID | Chimpanzee Marker Symbol | Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position |
Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Chimpanzee.rpt (sorted by chimpanzee chromosome, space-delimited) |
|
| 20. Dog and Mouse Orthology |
| Dog Chromosome | Dog Entrez Gene ID | Dog Marker Symbol | Mouse MGI Accession ID | Mouse Chromosome | Mouse cM Position |
Mouse Entrez Gene ID | Mouse Marker Symbol | Mouse Marker Name | Data Attributes |
|
| HMD_Dog.rpt (sorted by dog chromosome, space-delimited) |
|
| Gene Ontology Data |
|---|
1. Gene Ontology (GO) Annotations of Mouse Markers (tab-delimited)
(see also go_terms.mgi to translate GO IDs to GO terms)
Notice: as of 21-Aug-2009, MGI will be providing this daily gene_association.mgi file in GAF 2.0 format. This file has two additional columns, 16 and 17, explained in detail here.
A GAF 2.0 file can be easily converted to GAF 1 by the removal of the last two columns. Additionally, a GAF 1 version of this file which is updated weekly is available here. |
Database
Designation | MGI Marker Accession ID | Mouse Marker Symbol | NOT
Designation | GO
Term ID | MGI
Reference Accession ID | GO
Evidence Code | Inferred From |
Ontology
P=Biological Process
F=Molecular Function
C=Cellular Component |
Mouse Marker Name | Mouse Marker Synonyms
(if any) | Mouse Marker Type
gene
transcript
protein | Taxon | Modification Date | Assigned By |
|
| gene_association.mgi |
|
| 2. References used in GO annotations to mouse Markers (tab-delimited) |
| MGI Reference Accession ID | PubMed ID |
|
| go_refs.mgi |
|
| 3. GO terms and GO IDs for all three ontologies (Biological Process, Cellular Component, Molecular Function) (tab-delimited) |
|
|
| go_terms.mgi (only those terms annotated to MGI markers are included) |
|
| 4. GO annotations to mouse Markers that have human orthologs (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | Marker Name | GO ID | GO Term |
GO Evidence Code | PubMed ID | SWISS-PROT | GenBank ID
EMBL ID
DDBJ ID |
|
| MRK_GOHuman.rpt |
|
| 5. Marker/SWISS-PROT Associations for Markers with GO Annotations (tab-delimited) |
| MGI Marker Accession ID | SWISS-PROT ID (;-delimited) |
|
| gp2protein.mgi |
|
| 6. MGI genes that have been selected for comprehensive annotation as part of the GO Consortium Reference Genome Annotation Project (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol |
|
| go_ref_genome.mgi |
|
| 7. MGI genes for which curation is considered complete. Curation includes annotations derived from the biomedical literature as of the date listed (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | Date Completed |
|
| go_complete.mgi |
|
| 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. MGI Marker associations to Phenotype Annotations and Ensembl sequence information (tab-delimited) |
| MGI Marker Accession ID | Marker Symbol | Marker Name | Ensembl Accession ID |
High-level Mammalian Phenotype ID | Mammalian Phenotype Term |
|
| MRK_Ensembl_Pheno.rpt |
|
| 4. List of All Mouse Phenotypic 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 | High-level Mammalian Phenotype ID (comma-delimited) | Synonyms (pipe-delimited) |
|
| MGI_PhenotypicAllele.rpt |
|
| 5. 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 | High-level Mammalian Phenotype ID (comma-delimited) |
|
| MGI_QTLAllele.rpt |
|
| 6. 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 |
|
| 7. 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 |
|
| 8. 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 |
|
| 9. 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 |
|
| 10. Genotypes and Mammalian Phenotype Annotations for Marker Type Genes excluding conditional mutations (tab-delimited) |
| Allelic Composition | Allele Symbol(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID | MGI Marker Accession ID (comma-delimited) |
|
| MGI_GenePheno.rpt |
|
| 11. Genotypes with both Phenotype and Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) |
| Allelic Composition | Allele Symbol(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID | MGI Marker Accession ID (comma-delimited) | OMIM ID (comma-delimited) |
|
| MGI_Geno_Disease.rpt |
|
| 12. Genotypes with both Phenotype and Negated Disease Annotations for Marker Type Genes, excluding conditional mutations (tab-delimited) |
| Allelic Composition | Allele Symbol(s) | Genetic Background | Mammalian Phenotype ID | PubMed ID | MGI Marker Accession ID (comma-delimited) | OMIM ID (comma-delimited) |
|
| MGI_Geno_NotDisease.rpt |
|
| 13. Associations of Mouse Genes with OMIM Phenotypes |
| OMIM ID | OMIM Term | Synonyms (|-delimited) | Mouse Gene | Mouse Gene ID | Human Gene | Mouse only/Human only/Both |
|
| MGI_PhenoOMIM.rpt |
|