This work focusses on identifying which of the AltExtron splice junction isoforms and the isoform events are conserved in mouse. The approach used is as below.

I. Firstly we examined human exon constructs (obtained by concatenating exon regions flanking a splice junction) for acceptable matches with mouse transcript (ESTs and mRNAs) sequences and to derive the matching mouse exon constructs.

II. Secondly we examined whether these matching mouse exon constructs indeed as a splice junction on the mouse draft genome sequence. This was carried out by ascertaining that the matching mouse exon construct make a gapped alignment at the splice junction.

III. Conserved human alternative splicing events are delineated by applying the criteria that each of different splice junctions involved in a splicing event is conserved as per the above two methodologies.

The following data files are generated in this work.

I. IDENTIFICATION OF HUMAN EXON CONSTRUCTS THAT ARE ALSO SEEN IN MOUSE TRANSCRIPT SEQUENCES

I.1. Conserved constitutive introns : Conserved human constitutive introns are listed along with the accession numbers of the matching mouse transcript sequences (conserved_constitutiveIntrons.dat). The sequences of the human exon constructs along with the matching mouse exon constructs are given in (conserved_constitutiveIntrons_withHumanMouseSequences.dat).

I.2. Conserved alternative introns : Conserved human alternative introns are listed along with the accession numbers of the matching mouse transcript sequences (conserved_alternativeIntrons.dat). The sequences of the human exon constructs along with the matching mouse exon constructs are given in (conserved_alternativeIntrons_withHumanMouseSequences.dat).

II. EXAMINING THAT THE MATCHING MOUSE EXON CONSTRUCTS INDEED MAP TO A MOUSE SPLICE JUNCTION.

II.1 Summary of this analysis : given in the file mouseGenomeMatch_summary.html.

II.2 Data on the match analysis of mouse exon constructs with mouse genome sequence:

1. Human splice junctions that are unambiguously seen in mouse genes as well - conserved_altconIntrons_unambiguousEntries.dat and conserved_altconIntrons_unambiguousEntries.notes

2. Human splice junctions that are seen (with some ambiguity) in mouse genes also - conserved_altconIntrons_ambiguousEntries.dat

3. Lengths of the introns as seen in human and in mouse genes - lengths_conservedIntrons_humanMouse.dat

III. DELINEATED CONSERVED ALTERNATIVE SPLICE EVENTS.

III.1. Conserved alternative events (conserved_alternativeEvents.dat) : Human alternative splicing events that are conserved in mouse are listed.

III.2. Changes in the protein sequences due to the conserved alternative events (effects_onProteinSequences.dat) : Effects on protein sequences due to the conserved alternative splicing events are listed. For the events that caused use of alternative stop codon and alternate frame of translation, the human-mouse protein sequence alignments are given around the region of alternative stop codon and the region translated in alternate frame of translation.

III.3. Protein product names (genes_conservedEvents.dat) : Protein product names of the genes in which conserved alternative splicing events are observed.

Note: In all the files, the introns/exons are listed with the IDB identifiers.