NCF1 gene and its pseudogenes
Komatsuzaki, Shoko
Dear UCSC Team,
I am trying design PCR primers for NCF1 gene sequencing (human sample). For NCF1 gene, there are two pseudogenes are known (NCF1B and NCF1C). If I search “NCF1”, two chromosome positions appears (https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hgsid=243786907_SNZgdaASLzVp8aWqI6Tt1nj3IUea&org=Human&db=hg19&position=NCF1&pix=1655 , (chr7:74188309-74203720 and chr7_jh159134_fix:2303198-2318612). Are these the same ?
For NCF1B (one of the pseudogenes) there are also two positions (chr7:72634674-72649979 and chr7_jh159134_fix:749875-765181), (https://genome-euro.ucsc.edu/cgi-bin/hgTracks?hgtgroup_map_close=1&hgtgroup_genes_close=0&hgtgroup_phenDis_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_denisova_close=1&hgtgroup_varRep_close=0&hgtgroup_rep_close=0&hgsid=243786907_SNZgdaASLzVp8aWqI6Tt1nj3IUea&position=NCF1B&hgt.positionInput=NCF1B&goButton=go&hgt.suggestTrack=knownGene&db=hg19&c=chr7_jh159134_fix&l=749874&r=765181&pix=1655&dinkL=2.0&dinkR=2.0)
For the other pseudogene NCF1C is similar (two chromosomal positions, chr7:74572384-74587802 and chr7_jh159134_fix:2685814-2701234
I try to blast NCF1 gene to find specific sequences which don’t exist in NCF1B and NCF1C, but since sequences with chromosome positions starting with jh159134 are included in the blast results, it is difficult to understand what is happning.
What is actually chr7_jh159134_fix:?
Thank you in advance
Sincerely,
Shoko Komatsuzaki
Institute of Human Genetics
University Hospital Jena
Am Klinikum 1
07747 Jena Germany
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Luis Nassar
Hello, Shoko.
Thank you for your interest in the Genome Browser.
The chromosomes with the names chr#_*_fix, and chr#_*_alt, represent patches released by the GRC to improve the quality of the underlying region (_fix), or to add alternative sequences on areas that see particularly large amounts of variation (_alt), without changing the reference coordinates.
You may find the following FAQ entry helpful: http://genome.ucsc.edu/FAQ/FAQblat.html#blat1c
As you have seen, hg19 includes a large number of these patch regions (http://genome.ucsc.edu/cgi-bin/hgTracks?chromInfoPage=&db=hg19).
We offer a track which allows you to see where these patches are located, and also see them where they would exist in the entire chromosome. See the image below which is in 'Multi-region' display, meaning the area in in the ideogram between the two red boxes represents where the fix sequence fits.
We also have a track for hg19, Problematic Regions which points out peculiar locations of the genome, including patches and fixes.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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