I'm currently using the BioMart database to identify genes and regulatory elements based on chromosome and position coordinates.
However, I'm also interested in determining whether a given position falls within specific regions of a gene, such as exons, introns, or untranslated regions (UTRs). Are there any databases or tools available where I can input chromosome and position coordinates and obtain information about the specific gene region, like exon, intron, or UTR, that the position is located on? Thank you for any suggestions or recommendations!
In addition to identifying positions with regulatory roles (previous post), I also want to determine the specific gene regions (e.g., UTR, exon, intron) associated with the chromosome positions. The previous method only provided information on positions with regulatory roles, yielding 21 outputs out of about 70 chromosome:position inputs. For the remaining positions, I am interested in knowing their location within the gene, and whether they fall within UTRs, exons, or introns.
how is it different from your previous question ? Tool to Identify Gene, Regulatory Role, and Function at Integration Sites
In addition to identifying positions with regulatory roles (previous post), I also want to determine the specific gene regions (e.g., UTR, exon, intron) associated with the chromosome positions. The previous method only provided information on positions with regulatory roles, yielding 21 outputs out of about 70 chromosome:position inputs. For the remaining positions, I am interested in knowing their location within the gene, and whether they fall within UTRs, exons, or introns.
If you are already using BioMart then you should be able to get this information right in that db.