Hi Ilana, The phenomena you describe is most likely due to a duplication event that was inverted as well. In these cases, it can be hard to know to where a transcript maps to, especially if the duplication event occurred recently. When this happens a transcript may be shown as mapping to both genomic locations.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Ilana Livyatan" <[email protected]> To: [email protected] Sent: Tuesday, October 5, 2010 2:56:05 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Refgene table entries with same ID but different strand? Hello, I came across a few transcripts that have more than one entry in the refGene table of the mouse musculus mm9 annotation. What's interesting is that although the transcript ID is identical in the entries (NM_...) and the name2 field is also identical the strand field is opposite - the transcript appears to be both on the + and the - strand! How does this happen and what does it mean? Some examples: NM_178216 NM_013549 NM_175657 NM_001110555 If this is of any help, the transcripts belong to histone genes which are part of a cluster of many similar genes on chromosome 3 and 13. Thanks, Ilana Livyatan Dr. Eran Meshorer's Lab Department of Genetics Room 2-544, Givat Ram The Hebrew University of Jerusalem Jerusalem, 91904 ISRAEL Tel: 972-2-6585143 Fax: 972-2-6586975 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
