AlignTranscript ( Align mRNA, Genomic and Protein Sequence )
by Ivano Zara

This Application aligns the sequence of a transcript with the respective genomic sequence (which may also differ from that of the transcript) in a neighborhood of a chosen position.
The Application also aligns the translations of the genomic and transcript sequence (remember that they can be different).
You can also enter the coordinates in hgvs variant format (eg c.45del). In this case, the varied nucleotide and amino acid sequences will also be shown (the differences will be indicated in red).
HGVS with insertions or duplications or indels are used only for the position and the varied sequence is not aligned.
Try our example
Genomic realease hg38
Variant (HGVS mode) c.51C>T Gene: LMNA
Variant (HGVS mode) c.51C>T ID transcript: NM_170708
Gene Name: JUP ; Center in mRNA position 55


Show nt around the center
 
Genomic Release:

From Transcript
Variant (Hgvs mode )
    (hgvs format: c.'variant'; example c.45A>T ; c.65del ; etc.)
OR
Pos in mRNA
(format: -nn for 5'UTR ; *nn for 3'UTR ; nn for CDS)
Gene:
OR/AND
Transcript ID:
The name of the gene or ID transcript (NM_..) is required