Why Ucsc Refseq Gene Position Overlap Gap?

Question

[gqyi20]

Hello! everyone.

Recently, I downloaded chicken "refseq gene" file and "gap" file in UCSC, but I found some gaps overlapping refseq genes, even locating in genes, so what happend in this situation and why? Wheather we can discard those genes overlapping gaps or not? I can't search similar question about this, so I need your help. Thanks a lot!

A example is showed as follows:

refseq gene
#bin   name               chrom      strand    txStart txEnd
74     NM_001199320        chr1           -    1371140    1821501
gaps
chrom     chromStart    chromEnd     size
chr1      1581252       1614100     32848
chr1      1615830       1637787     21957

[Pavel Senin]

I don't know about the chicken sequence, but, theoretically, "gap" can be anywhere indicating that the underlying sequence is not known for some reasons and should be filled with Ns. Edit: I think you can check this by looking at FASTA at the gap's positions.

[k.nirmalraman]

you can also align the sequences from refseq to the chicken genome to see the alignment.

Answer 1

[deanna.church]

The chicken assembly is a whole genome shotgun assembly and thus contains many gaps. In this view from the NCBI alignment (which may differ from the UCSC alignment): http://tinyurl.com/n2onshb

The second track is the 'Tiling Path' track and shows the order of WGS contigs and the gaps between them in this assembly.