A closer look

The gene summary view in more detail

Let's look more in depth at the figure on the gene summary view (Figure 11). 

The gene summary view in more detail
Figure 11. The lower half of the display depicts all transcripts in the genomic region.

Name, synonyms, etc. The official gene name is displayed at the top, along with other names and symbols the gene is known by. For human genes, the official gene name comes from the HGNC (HUGO Gene Nomenclature Committee).

BRCA2 has one coding sequence in the CCDS set.  Havana manual curation is available for this locus, and the link to the BRCA2 gene in Havana is given.

BRCA2 Transcripts. All transcripts in the region are displayed. Gold and red transcripts [A] are protein coding whilst blue, pink and grey transcripts are non-coding. The gold transcripts indicate a Havana/Ensembl merge. In this case, BRCA2-001 is gold, indicating the sequence is agreed on by both projects. A help page explains the colours more in depth.

Transcript structure. Boxes are exons, and connecting lines are introns. Filled boxes indicate coding sequence, while unfilled boxes are UTR(UnTranslated Regions).

For example, the transcript above is gold, showing it's a protein coding transcript (Havana/Ensembl merge). It has two exons. Both exons have filled and unfilled regions, meaning both exons contain coding sequence and UTR. The intron is a line between the exons.

Transcripts drawn above the blue bar (genome) are on the forward strand of the chromosome (like BRCA2), and transcripts drawn underneath (like the neighbouring N4BP2L transcripts, [B]) are on the reverse strand of the chromosome.