Hello, Rajesh. I found a few pieces of information when searching for FSBP. First, I searched for NM_006550 in hg18 and got no results. Next, I browsed to the coordinates you specified in hg18 (chr8:95,513,351-95,518,308) and in the RefSeq Genes track, which is what the file refGene.txt is based on, the only items present are three transcript variants of RAD54B (NM_012415.3, NM_001205262.1 and NM_001205263.1). A search for NM_006550 on the NCBI site revealed that this entry has actually been removed from their database (http://www.ncbi.nlm.nih.gov/nuccore/NM_006550).
In our Browser, a search for FSBP did show that there is an entry in the UCSC Genes track, but this track has not been updated since 03 March 2009 while the RefSeq Genes track was updated on 02 January 2012. You can determine when a track was last updated in two ways: either click the gray bar on the left side of the Browser's graphical display or click the track name in the track listings below the graphical display. You will see "Data last updated" near the top of the page. The fact that you found NM_006550 in the Browser makes me wonder if you were actually using our site at http://genome.ucsc.edu or one of our mirror sites which may not be updated as regularly. It is possible that the other items that you did not find in refGene.txt have been similarly removed from the NCBI database. A simple search of your RefSeq IDs at http://www.ncbi.nlm.nih.gov/nuccore/ will reveal whether or not this is the case. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: Patidar, Rajesh (NIH/NCI) [C] [mailto:[email protected]] Sent: Wednesday, January 04, 2012 6:56 AM To: [email protected]; [email protected] Subject: RE: [Genome] Missing genes in refGene.txt file Hi Steve, Thanks for writing back. I re-downloaded the refGene.txt file today and was trying to grep "FSBP" from it which is not in file but I can see it in genome browser (chr8:95,513,351-95,518,308) NM_006550. Thanks, Rajesh Patidar(NIH/NCI)[C] -----Original Message----- From: Steve Heitner [mailto:[email protected]] Sent: Tuesday, January 03, 2012 5:36 PM To: Patidar, Rajesh (NIH/NCI) [C]; [email protected] Subject: RE: [Genome] Missing genes in refGene.txt file Hello, Rajesh. The file you downloaded is the most current version. The RefGene table and its associated download file are updated regularly. The version of the file you referenced is for the human assembly hg18. I performed a search in the Browser for MOD2 and KRC in hg18. I found no results for MOD2, but I did find LMOD2, TMOD2 and ELMOD2. I also found no results for KRC, but I did find KRCC1. This is consistent with the contents of the refGene.txt file and the NCBI database. Could you please provide a specific example of a search result that you found in the Browser (including RefSeq ID) but did not find in refGene.txt? Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Patidar, Rajesh (NIH/NCI) [C] Sent: Friday, December 23, 2011 10:12 AM To: [email protected] Subject: [Genome] Missing genes in refGene.txt file Hi, I downloaded the the refGene.txt file from ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ and was looking for a list of genes I have and wanted to know there coordinates but the list I have, is longer than the refGene.txt's gene list. For example I cannot find MOD2 or KRC and many more. But I can get them on genome browser. I am wondering where I can get the most complete list of human genes build 18 and there coordinates. Happy Holidays, Thanks, Rajesh Patidar(NIH/NCI)[C] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
