The Genome Browser offers several ways to highlight gaps in alignments
of query sequences (usually transcripts) to the genome. Gaps
result from sequences in the genome or query (or both) that cannot
- double horizontal line (=): both the genome and query have unalignable
sequence between regions of aligned sequence, a double-sided insertion. If
this option is not selected, it will display as a single horizontal line.
- orange lines or
purple lines: unalignable query sequence, orange
for the middle of a sequence and purple for the beginning or end.
- green lines: poly-A tail or poly-T head that
does not align to the genome.
When zoomed out past the base level, the browser chooses one color to
represent many bases. The priority of display, from most important to least
different mRNA base/nonsynonymous codon coloring
different item bases
unalignable query sequence (orange or purple), an insertion in
both genome and query (double horizontal line), and a poly-A tail (green).
The browser will not display
genomic/mRNA codon coloring when
viewing large regions of the genome.
Interpretation of Display
Gaps are usually due to a deletion or insertion in one or both sequences,
or, infrequently, a problem in the sequencing. Often, the genome will have a
large "insertion" relative to a query (single horizontal line) that is
actually an intron.
Double-sided insertions (double horizontal line) are unusual and may indicate
an assembly error, sequencing error, or polymorphism.
Unalignable query sequence in the middle of a query (orange) implies extra
bases in the transcript sequence or missing bases in the genome sequence.
Insertions at the beginning or end of a query (purple), implies a partial
alignment of the query. For instance, a very short sequence next to large
intron gap may be incorrectly aligned. Unalignable query
sequence may also be due to polymorphisms.
Poly-T heads result from queries that are the reverse complement of the genomic
sequence. Poly-A tails and poly-T heads (green) of mRNAs usually can not be
aligned to the genome; this is a special case of an unalignable query sequence.
For information about mRNA codon and base coloring, click
For information about EST base coloring, click