Hello Nuala, You are correct, the sequence associated with accession AK129600 is included in the Human mRNAs track in hg17, but not in hg18 or hg19.
There are a two reasons for this. 1) The genomic reference sequence that this mRna sequence aligns to is completely masked as a long terminal repeat by Repeat Masker (http://en.wikipedia.org/wiki/Long_terminal_repeat). To view this, a) obtain the sequence from the Genbank report ( http://www.ncbi.nlm.nih.gov/nuccore/34526172 ) b) perform a web Blat (http://genome.ucsc.edu/cgi-bin/hgBlat) c) click from the results page through the "browser" link d) make sure the RepeatMasker track is set to display "full" This is true for any of human genomes (hg17/18/19). To see the details of the repeat annotation, click through to the RepeatMasker details page from the Assembly browser display of the annotation. 2) Sequences that are comprised completely of repeat masked sequence are not retained in the mRNAs track. This filtering rule was implemented late 2005. This is why the data remains in the earlier assembly (hg17) but is not and never was included in the later datasets (hg18, hg19). A work around would be to follow the same steps as in #1 above. Web Blat runs against unmasked genomic and the results can be saved as a custom track (and added to a Session for more permanence on the UCSC server). We noticed that several other sequence from the same source, also representing Hypothetical protein FLJ26089, are included in the newer database's mRNAs tracks. It may be that one of these would be a good substitute sequence for your analysis, if not already included. And lastly, know that any consensus sequence that you create from these inputs can be loaded as a custom track (as a complete transcript, even when spanning an annotated repeat region). http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions We hope this helps to explain the data and provides you a useable work-around, but please let us know if you have any followup questions, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Nuala Sykes" <nsy...@well.ox.ac.uk> wrote: > From: "Nuala Sykes" <nsy...@well.ox.ac.uk> > To: gen...@soe.ucsc.edu > Sent: Tuesday, January 12, 2010 8:48:57 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Human Gene AK129600 > > Hello, > > The Human Gene AK129600 (Hypothetical protein FLJ26089) was removed > from the UCSC genome browser between versions May 2004 and March > 2006. Could you tell me the reason for this please? > > Thank you, > Nuala > > > > _______________________________________________ > Genome maillist - Genome@lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
