Choose Transcript For Free

Stable IDs are created in the form ENS[species prefix][feature type prefix][a unique eleven digit number]. For example a mouse gene might be ENSMUSG###########. This means that we can immediately tell from a stable ID what kind of feature they refer to and what species they are in.

Isoforms refers to different versions of protein from the same gene in this setting, and transcript variants refers to different versions of mRNA transcript from the same gene.

Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule. RNA polymerase is the main transcription enzyme. Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).

DNA transcription is the process by which the genetic information contained within DNA is re-written into messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it acts as the basis for the translation of DNA.

The identifier that is assigned (GeneID) is an integer, and is species-specific. In other words, the integer assigned to dystrophin in human is different from that in any other species. The GeneID is reported in RefSeq records as a 'db_xref' (e.g. /db_xref='GeneID:856646', in GenBank format).

Why do they differ? While Ensembl gene models are annotated directly on the reference genome, RefSeq annotates on mRNA sequences. Due to sequence differences between the reference genomes and individual mRNAs, some of the RefSeq mRNAs may not map perfectly to the reference genome.

As for finding multiple transcripts for a given gene, this is the result of alternative splicing, which is part of what contributes to making an organism (such as ourselves) so complex with a relatively small number of genes.

NCBI allows users to view annotations in a tabular format that can then be downloaded into a text file. Ensembl's BioMart [24] and the UCSC Table Browser [25] allow for both simple downloads of annotations and for quite complex datasets to be generated.

Each transcript ID includes a unique, stable 11 digit number. Transcripts beginning with ENST are human transcripts (for example, ENST00000369985). A three-letter code is inserted for other species; (for example, ENSMUST defines a mouse transcript).

Many genes have more than one transcript due to alternative splicing. We refer to the various transcripts (splice variants) for a particular gene as transcript variants.