Author: Editor

Gene Resources
Gene News

Announcements from the Gene database, including data content, web features, FTP site and tools.

• Orthologs to be expanded to include insects May 10, 2024
  Reports of orthologous genes are being expanded to include insects versus D. melanogaster (txid7227) in both the web pages and the gene_orthologs.gz file on the Gene FTP site. These insect orthologs are computed using the same process as the other orthologs, described here. The interim gene_orthologs_supplemental.gz FTP file will be removed within the next t […]
• Updates to the UniProtKB FTP file November 2, 2023
  The gene_refseq_uniprotkb_collab.gz file on the Gene FTP site reports matched pairs of NCBI RefSeq and UniProtKB accessions. With a new process to find UniProtKB and RefSeq proteins related to each other, this file now reports data for over 170 million RefSeqs. This update introduces three additional columns.First, columns are being added for both the NCBI T […]
• CCDS release 24 for human is public in Gene October 31, 2022
  ​​The Consensus Coding Sequence (CCDS) update that compares the NCBI Homo sapiens annotation release 110 to the Ensembl​ release 108 was released last week, and this update is now reflected in Gene as well. This update adds 2,746 new CCDS IDs, and adds 237 genes into the human CCDS set. CCDS Release 24 includes a total of 35,608 CCDS IDs that correspond to 1 […]
• Gene Information from the Alliance of Genome Resources January 26, 2022
  ​NCBI Gene has added descriptive information about genes from the Alliance of Genome Resources for organisms that include Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, and Saccharomyces cerevisiae. Links to gene pages at the Alliance of Genome​ Resources are provided in the Summary section in the […]
• Annotation Matches with Ensembl Rapid Releases October 22, 2021
  NCBI Gene has added Ensembl Rapid Releases to the calculation of matching annotations between NCBI RefSeq and Ensembl. This has resulted in the inclusion of over 60 additional assemblies for a total of 241 organisms represented in the set. Matches are made based on transcript and CDS comparisons, and Ensembl gene, transcript, and protein identifiers for anno […]
• CCDS release 23 for mouse is public in Gene October 28, 2019
  ​The Consensus Coding Sequence (CCDS) update that compares NCBI's Mus musculus annotation release 108 to Ensembl's release 98 was released last week, and this update is now reflected in Gene as well. This update adds 1,570 new CCDS IDs, and adds 175 genes into the mouse CCDS set. CCDS release 23 includes a total of 27,219 CCDS IDs that correspond t […]
• FTP change March 28, 2019
  In accordance with changes in the representation of lineage in the Taxonomy database, the following subsets of data for viruses will no longer be available separately in the ASN_BINARY and GENE_INFO directories on the Gene FTP site:dsDNA viruses, no RNA stagedsRNA virusesssDNA virusesssRNA negative-strand virusesssRNA positive-strand viruses, no DNA stageDat […]
• Vega links to be removed December 4, 2018
  The Vega website, which was maintained by the HAVANA group at the Wellcome Trust Sanger Institute, has been archived, as per this announcement.  Consequently, our links to matching Vega ​sequences and genes are being removed.  This change will occur within the next week.The gene2vega.gz file on our FTP site will be retained, but is no longer being updated. […]
• CCDS release 22 for human is public in Gene June 15, 2018
  The Consensus Coding Sequence (CCDS) update that compares NCBI's Homo sapiens annotation release 109 to Ensembl's release 92 was released this week, and this update is now reflected in Gene as well. This update adds 894 new CCDS IDs, and adds 154 Genes into the human CCDS set. CCDS release 22 includes a total of 33,397 CCDS IDs that correspond to 1 […]
• More expression data in Gene January 25, 2018
  The gene expression data that was announced last February is now being made accessible in more ways: We've added a brief sentence to the Summary section describing the expression pattern. It's now possible to query for genes with particular expression patterns. We've expanded the data, initially available for human, mouse and rat, to include p […]
• New FTP file for orthologs November 28, 2017
  Orthologous genes and other types of gene groups are currently reported in the gene_group file on the Gene FTP​ site. For ease in accessing the orthology data subset, a new gene_orthologs FTP file has been created, which uses the same format as the gene_group file.The ortholog records will continue to be represented in the gene_group FTP file for a period of […]
• HIV-1 update October 10, 2017
  The HIV-1 interaction datasets available in NCBI's Gene resource have been updated with data provided by the Southern Research Institute (SRI).For the protein interactions dataset:8,005 interactions16,215 interaction descriptions3,859 proteins encoded by 3,757 human genes6,822 publications. For the replication interactions dataset:1,595 interactions1,85 […]
• RefSeq Functional Elements in Gene June 20, 2017
  NCBI is pleased to announce the initial data release of RefSeq Functional Elements, a resource that provides RefSeq and Gene records for experimentally validated human and mouse non-genic functional elements. For further information, please see the recent NCBI Insights blog and the RefSeq Functional Elements website.Gene records for these elements include a […]
• Update to gene2xml utility March 1, 2017
  If you use the gene2xml utility to read files from the ASN_BINARY directory on the Gene FTP site, please download the latest revision (1.6) here. This update will be needed to read new data elements that will be added to the ASN.1 in the near future.To see which version of gene2xml you are currently using, simply run gene2xml with a single hyphen as a parame […]
• Expression data in Gene February 27, 2017
  NCBI's Gene resource has added a new feature to report normalized RNA expression levels computed from RNA-seq data for human, mouse, and rat genes. Expression data can provide key insights into where and when a gene may be functioning, for example by exposing the correlation between expression of human SLC25A4 and its established role in heart function, […]