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Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online. [5] Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. [6] Ensembl and Ensembl Genomes software uses an Apache 2.0 license [7] license.
[1] [5] [6] The GeneCards database provides access to free Web resources about more than 350,000 known and predicted human genes, integrated from >150 data resources, such as HGNC, Ensembl, and NCBI. The core gene list is based on NCBI, Ensembl and approved gene symbols published by the HUGO Gene Nomenclature Committee (HGNC).
Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, [7] and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data.
Users can select various types of identifiers such as CCDS ID, gene ID, gene symbol, nucleotide ID and protein ID to search for specific CCDS information. [1] The CCDS reports (Figure 1) are presented in a table format, providing links to specific resources, such as a history report, Entrez Gene [ 10 ] or re-query the CCDS data set.
Also, the GENCODE website contains a Genome Browser for human and mouse where you can reach any genomic region by giving the chromosome number and start-end position (e.g. 22:30,700,000..30,900,000), as well as by ENS transcript id (with/without version), ENS gene id (with/without version) and gene name. The browser is powered by Biodalliance. [19]
Gene Annotator: The Gene Annotator or GA tool takes as input a list of gene symbols, RGD IDs, GenBank accession numbers, Ensembl identifiers, or a chromosomal region and retrieves gene orthologs, external database identifiers and ontology annotations for the corresponding genes in RGD. The data can be downloaded into an Excel spreadsheet or ...
Ensembl: UniProt: RefSeq (mRNA) NM_001009923 NM_001009924 NM_001009925 ... This gene encodes a multi-pass transmembrane protein that belongs to the TMEM134/TMEM230 ...
340061 72512 Ensembl ENSG00000184584 ENSG00000288243 ENSMUSG00000024349 UniProt Q86WV6 Q3TBT3 RefSeq (mRNA) NM_001301738 NM_198282 NM_001367258 NM_001289591 NM_001289592 NM_028261 RefSeq (protein) NP_001288667 NP_938023 NP_001354187 NP_001276520 NP_001276521 NP_082537 Location (UCSC) Chr 5: 139.48 – 139.48 Mb Chr 18: 35.87 – 35.87 Mb PubMed search Wikidata View/Edit Human View/Edit Mouse ...