![]() ![]() If that gene is associated with Mendelian disorders that have a different MIM number, that MIM number will not be provided in gene_info.gz.īoth types of MIM numbers associated with Gene records are reported in the ftp file mim2gene. The gene_info.gz file provided from the Gene ftp site includes the MIM number associated with the gene. Symbols used by OMIM for genes and diseases are intermingled in Gene's Gene aliases section. Within the body of the record, the MIM number associated with the gene is reported in the See Related and Additional links sections a MIM number associated with a disease may be reported in the Phenotypes section, along with the name of the condition. ![]() Links provided from the Links menu in the upper right-hand part of the Gene record are based on both types of MIM numbers. Gene integrates information from OMIM, and creates links to OMIM, at two levels: 1. The official name is reported in the comprehensive gene_info file on the FTP site (note also the species-restricted ones in the GENE_INFO subdirectory. In those cases, the species-specific nomenclature is provided, but not as the default. In some instances, this is at variance with the symbol assigned by species-specific nomenclature committees. NOTE: To the greatest extent possible, each protein-coding gene in mitochondria has been assigned the same name (symbol) and full description across species. Gene and RefSeq encourage all data submitters to conform to the suggestions from major sequence databases. The terms can be considered equivalent, and reflect primarily the source of the naming. The terms that are used should not be construed to indicate different types of uncertainty. When the name that should be assigned to the gene or protein is uncertain, sources use different conventions. Because the sequences represented by NCBI's predictions are provided in accessions beginning with XM_ or XP_ or XR_, you might assume that all accessions with that format would have names beginning with 'similar to '. If a significant match is found, and the name is informative, then the automatic annotation process previously constructed the name of the model by combining 'similar to ' and the name of the matching protein. The protein sequences are compared to public protein sequence records from several model organisms. When NCBI automatically annotates a genome, it predicts both mRNAs and the proteins they encode. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. In other words, please consider use of the GeneID rather than a symbol as the stable identifier of a gene. If the same symbol has been assigned to different genes, and a nomenclature committee has not provided a unique name for these genes, Gene will not impose its own solution. Gene does not enforce uniqueness in preferred symbols. The nomenclature status of the name, where The current official symbol or database identifier if no official symbol is available 3. For example, if you transferred the gene_info.gz file to a unix or linux file system, the command You can therefore convert any GeneID into its current names by using the definitions provided in the file available as. ![]() It may help to consider that the Gene GeneID is unique across all taxa. The symbols seen in Genome Data Viewer and RefSeqs for contigs, scaffolds, and chromosomes, however, should be the same, because all are updated only with each major re-annotation of a genome. RefSeq, for example, does not resubmit the full annotation of a genomic sequence to the nucleotide database each time a symbol changes. You may notice, for example, that symbols in genomic RefSeq annotation, Genome Data Viewer, HomoloGene or UniGene, and their respective ftp sites, are not the same as those you see in Gene. Updates to names in Gene are not propagated immediately to all other resources in NCBI. Gene attempts to maintain current nomenclature. ![]()
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