Do antisense transcripts have different names than their sense strand transcripts?
If the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession NR_027920 while the sense transcript of the same gene is NM_010835.

In general, each transcript that is transcribed from a given locus has a different accession. The same is true for alternatively spliced transcripts. If a given gene has 4 AS transcripts, each of these transcripts will have a different, unique accession. The human insulin receptor gene, for example, has two protein coding transcripts, each with its own accession: NM_000208 and NM_001079817.

You may be interested in a recent analysis of cis-NATs in 10 species[1] and also in NATsDB: Natural Antisense Transcripts DataBase[2].


Osato N, Suzuki Y, Ikeo K, Gojobori T. 2007. Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics, 176(2): 1299-1306, doi:10.1534/genetics.106.069484.
Li JT, Zhang Y, Kong L, Liu QR, Wei L. 2008. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, 36(15):4833-44, doi:10.1093/nar/gkn470.