ATD - Mouse Release 1 (31 May 2005)

The data in his release is generated for all genes as annotated in Ensembl Mouse 27.33c.1. The extracted nucleotide region includes the gene region as defined in EnsEMBL. Such a region is extended both at the 5' and 3' ends by 3000 bases. Mouse EST and mRNA (transcript) sequences are mapped to these extended gene regions. Transcript confirmed introns and exons are delineated from these alignments.

Each transcript is then scrutinised for the presence of a polyA tail, and for the presence of polyA sites upstream of the cleavage site. Each transcript that has both a polyA tail and a polyA site is then taken and grouped with other such transcript within the same gene. Transcripts that conform to same splicing and use of same terminating polyA sites are grouped together in a class; a representative of which is called Transcript Pattern. The such Transcript Patterns are presented in the 'ATClasses' file as described below. This is the AltTrans data set.

Beside the Alternate Transcript classes, we also have a merged file that was created by using the AltPas data from Daniel Gautheret and the PolyA/cleavage sites found by the AltTrans method. That file, which we call 'merged_polya', has the polyA sites grouped by the cleavage site.

Splice Patterns for these genes are presented in our AltSplice web pages (namely http://www.ebi.ac.uk/asd/altsplice).

In this release the following data files are available:

Downloads
AT Classes (1Mb, gzip)	The AltTrans data set which contains alternate transcript patterns with annotation which PAC (PolyA Cleavage site), PAS (PolyA Signal), and which motif are used.
Merged polyA (15Mb, gzip)	The merged polyA file which contains for each EST/mRNA the PAC, PAS, motif, together with an indication whether the data is originating from AltTrans or AltPas.

AT Classes file

The AT Classes file lists for each gene groups of EST/mRNA sequences that conform to a unique Transcript Pattern; multiple transcript patterns differ from one another in either splicing or/and terminating polyA site.

For each group the PAC and PAS location are listed (local to our gene), and the PAS motif is given as well.

Merged polyA file

The merged polyA file lists for each gene all the identified polyA sites (either through AltTrans pipeline or through AltPas).

Transcripts are grouped by cleavage (PAC) location, and for each transcript a number of annotations are available separated by a tab, e.g. whether the transcript is an EST or mRNA, what EST library, clone name, the transcript's PAC, and in case of AltTrans also the gene structure.

 

AT Classes file

The AT Classes file lists for each gene groups of EST/mRNA sequences that conform to a unique Transcript Pattern; multiple transcript patterns differ from one another in either splicing or/and terminating polyA site.

For each group the PAC and PAS location are listed (local to our gene), and the PAS motif is given as well.

Merged polyA file

The merged polyA file lists for each gene all the identified polyA sites (either through AltTrans pipeline or through AltPas).

Transcripts are grouped by cleavage (PAC) location, and for each transcript a number of annotations are available separated by a tab, e.g. whether the transcript is an EST or mRNA, what EST library, clone name, the transcript's PAC, and in case of AltTrans also the gene structure.

 

AT Classes file

The AT Classes file lists for each gene groups of EST/mRNA sequences that conform to a unique Transcript Pattern; multiple transcript patterns differ from one another in either splicing or/and terminating polyA site.

For each group the PAC and PAS location are listed (local to our gene), and the PAS motif is given as well.

Merged polyA file

The merged polyA file lists for each gene all the identified polyA sites (either through AltTrans pipeline or through AltPas).

Transcripts are grouped by cleavage (PAC) location, and for each transcript a number of annotations are available separated by a tab, e.g. whether the transcript is an EST or mRNA, what EST library, clone name, the transcript's PAC, and in case of AltTrans also the gene structure.