Splicing Sequences Finder
Splice site analysis

Choose Ensembl Transcript ID (e.g. ENST00000357033):
or Gene Name (e.g. DMD):
or Ensembl Gene ID (e.g. ENSG00000198947):
Automatically select the longest transcript:	Yes No
Search for SNPs related to the analyzed sequence:	Yes No
Number of intronic nucleotides surrounding the exon (min: 20, max:1000):

into the following box ( characters remaining):

Your sequence must be at least 9 nucleotides long.

You can highlight a specific section of your sequence. For this, please specify the first and last nucleotide positions:

• First nucleotide
• Last nucleotide

This form allows you to perform an analysis on a sequence to find potential donor and acceptor splice sites. It can be followed by a SNP search.

Select a sequence

You can either choose a transcript or a gene to perform a sequence analysis. If the gene has several transcripts, an intermediate screen will allow the selection of a single transcript. Please note that if you have difficulties finding a gene using a gene symbol, you can check the HUGO Gene Nomenclature Committee for its proper symbol.

Automatically select the longest transcript

If you are sure that you must perform an analysis on the longest transcript of a given gene, this option will force the system to choose the longest transcript for you. Please note that if at least two transcripts match the requirement of being the longest, a screen will be displayed for you to choose the correct one. Default value: Yes.

Single Nucleotide Polymorphisms

Splicing Sequences Finder is able to check on Ensembl variation database for SNPs related to the analyzed sequence. Default value: Yes.

Nucleotides surrounding the exon

You can decide to display intronic nucleotides surrounding the exon. By default SSF will use a value of 0. Intronic nucleotides are limited to 1000 at 5' and 3' ends of the exon. If you type a value superior to 1000, the system will automatically change it to 1000. Default value: 0.

Paste your own sequence

Insteed of using our database, you can paste your own sequence. Before analyzing your sequence, the system will clean it and remove all characters that aren't A, C, G or T.
If you specify two nucleotide positions, SSF will highlight the sequences comprised between this two positions. The 0 values disable this option. Default value: 0.