[Genome] How does UCSC hg19 gene model add exons to RefSeqs?

[Dan Richards]

Hi, when using the human reference hg19 gene model, there are like this (in
GTF output format from hgTable Genes and Gene Prediction group, RefSeq
Genes track):

chr10   hg19_refGene    start_codon     135480472       135480474
0.000000        +       .       gene_id "NM_012147"; transcript_id
"NM_012147";
chr10   hg19_refGene    CDS     135480472       135481677
0.000000        +       0       gene_id "NM_012147"; transcript_id
"NM_012147";
chr10   hg19_refGene    exon    135480432       135481677
0.000000        +       .       gene_id "NM_012147"; transcript_id
"NM_012147";
chr10   hg19_refGene    CDS     135484982       135485230
0.000000        +       0       gene_id "NM_012147"; transcript_id
"NM_012147";
chr10   hg19_refGene    stop_codon      135485231       135485233
0.000000        +       .       gene_id "NM_012147"; transcript_id
"NM_012147";
chr10   hg19_refGene    exon    135484982       135485275
0.000000        +       .       gene_id "NM_012147"; transcript_id
"NM_012147";
where the hg19 model has an exon that does not exon exist in the RefSeq
accession (or any historical version of the RefSeq accession).

How/why does the alignment introduce an intron in this case? Does it ensure
there are plausible flanking splice junctions before inserting an intron to
a RefSeq sequence that lacks it but it maps to?

Dan
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