Explaining by way of example:

The flat file of acceptor splice sites, with information about
putative polypyrimidine (PPT) and U2 Branch Point (BP)
sequences, contains entries of the form:


>IDB1072296.1230
GB_MAP: IDB1072296 = A06939.1 (1..5322)
PROD:   furin
AGEZ:   27
ROI:    1181..1265  ->  -50..34
AG:     -50, -47, -29, -2, 3, 35,
PPT:    -42..-33, -23..-5, 5..14,
U2BP:   -31 [5.49], -24 [5.2], 11 [4.58],
SEQ1:   agaaggcaCTCTGTGCCTgacagctgaCCCTACCTTCCCTGTCCCCacag
SEQ2:   tgagCCACTCATATggctacgggcttttggacgcag
END


Where:

>IDB1072296.1230

    gives the altExtron identifier for the gene (IDB1072296), with
    the acceptor (3') splice site position (1230) representing the 
    position of the final nulceotide in an intron

GB_MAP: IDB1072296 = A06939.1 (1..5322)

    is the mapping to the GenBank entry from which this gene was
    derived. "A06939" is the accession; ".1" is the version; and
    "(1..5322)" is the position. In the case that the entry is
    on the complement strand in GenBank (always sense in altExtron)
    then the mapping will be set as: complement( .. ).

PROD:   furin

    is the gene product as best as we are able to parse it from
    the GenBank flat files.

AGEZ:   27

    is the AG "Exclussion Zone", being the number of nucleotides
    upstream from the end of the intron to the first AG other
    than the acceptor splice site itself. This parameter is of
    interest because it helps to define the region in which we
    expect to find the branch point and PPT.

ROI:    1181..1265  ->  -50..34

    is the "Region of interest", being arbitarilly defined as
    being from 3 AG's upstream of the splice site to 2 AG's
    downstream. The first set of co-ordinates give this region
    in terms of the gene overall, ane the second set give this
    region relative to the splice site (with no position 0).

AG:     -50, -47, -29, -2, 3, 35,

    are the relative positions of the AG nts in the ROI, including
    the splice site itself at -2.

PPT:    -42..-33, -23..-5, 5..14,

    describes the positions of pyrimidine rich tracts that we take
    as putative PPTs.

U2BP:   -31 [5.49], -24 [5.2], 11 [4.58],

    are the positions of putative U2 Branch Point Sequences. The
    number in the [] brackets is the bit score generated for this
    site based on a weight matrix analysis.

SEQ1:   agaaggcaCTCTGTGCCTgacagctgaCCCTACCTTCCCTGTCCCCacag

    is the intronic sequence part of the ROI with the putative
    PPTs in upper case.

SEQ2:   tgagCCACTCATATggctacgggcttttggacgcag

    is the exonic sequence part of the ROI.

END

    is a tag helpful in file parsing that indicates end of record


Full details of the PPT and BP prediction methods may be found
in the associated publications.


In the above example the AGEZ is 27, and as such we can expact the 
branch point to be no further than about 10-15 nts upstream of this
AG, otherwise we would expect this AG to be used for splicing. We see
that there is a putative PPT from -5 to -23, and then a putative BP
at -24, and another at -31. We thus suppose that this PPT is correctly
identified, but have two candidate BP positions.