Special rendering for discrepancies between propagated genomic annotation and available transcript data used for the annotation

There are number of cases when propagated annotation shows reasonable similarity to the best available transcript hit (but is not 100% identical). For such cases the following rendering has been implemented:

• mismatched codons are shown in red color
• mismatched nucleotide bases are printed over RNA bar
• mismatched amino-acids are printed over CDS bar
• deletions are shown as dashes '-' inside of RNA bar and CDS bar
• insertions are shown as hourglass-like triangles inside of RNA bar and CDS bar

Special case: ribosomal slippage If translation is known to be effected by ribosomal slippage, frameshifts can be seen as shifted (but not colored) codons and corresponding amino acids.

RefSeq coding region with mismatches, deletion, and insertion in the genomic feature compared to the genomic sequence

Observe RefSeq coding region with mismatches, deletion, and insertion in Sequence Viewer

RefSeq RNA with insertion, deletion, or mismatch in the genomic feature compared to the genomic sequence

Observe RefSeq RNA with insertion, deletion, or mismatch in Sequence Viewer .

Ribosomal slippage with -1 frameshift

Ribosomal slippage is represented by an extra "joinvisual" shift of the translated sequence.

Note how NP_001120696.2's AAA(K) codon is shifted relative to NP_001103414.2's AAC(N) because of -1 frameshift.

Observe Ribosomal slippage with -1 frameshift in Sequence Viewer

Ribosomal slippage with +1 frameshift

Note the gap in CDS bar because of +1 frameshift.

Observe Ribosomal slippage with +1 frameshiftin Sequence Viewer