[Genome] diference between manual and displayed BLAT mapping

[ines mollet]

Hi,
the mapping which comes in the tables downloaded from
UCSC for BF245832 (hg18) has only exons 1 and 2 and
then a third block which corresponds mostly to exon 17
with the ag nucleotides of the 3' splice site included
in the block, which results in a non consensus splice
site 

106	609	4	0	1	8	53	13	89821	+	BF245832	918	1	668	chr11
134452384	35117296	35207731	18
29,54,14,19,48,104,97,39,30,31,16,23,7,55,20,12,11,5,
1,30,84,98,121,196,301,398,437,468,499,515,550,558,613,639,651,663,
35117296,35154724,35154779,35154794,35154815,35207249,35207353,35207451,35207491,35207521,35207553,35207570,35207611,35207618,35207674,35207702,35207715,35207726,


The manual BLAT mapping of this sequence gives
splicing exons 1,2,16 and 17

The result of the manual BLAT mapping is better and
has fewer query inserts - the blocks and positions
with parenthesis added bellow correspond to the
mapping of exon 16 which is missing in the mapping
displayed on the browser

635	4	0	1	8	27	14	89795	+	BF245832	918	1	668	chr11
134452384	35117296	35207731	20
29,54,14,19,48,(12,16),102,97,39,30,31,16,23,7,56,19,12,11,5,
1,30,84,98,121,169,182,198,301,398,437,468,499,515,550,558,614,639,651,663,
35117296,35154724,35154779,35154794,35154815,(35199827,35199839),35207251,35207353,35207451,35207491,35207521,35207553,35207570,35207611,35207618,35207675,35207702,35207715,35207726,


Why does this happen? What parameters do you apply in
a manual BLAT  mapping which make it better than the
BLAT mappings displayed on the browser?


Thank you for your attention

Ines


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