Investigating Intergenic Splice Forms Using SynaMap™
SynaMap™ is an application designed for accurately mapping transcript data to genome sequences. It provides fast and accurate identification of exon positions and splice sites within a particular genome.
Application Example:
Alternatively spliced genes are known to contribute to transcript variation within genomes. However, recent research based upon EST analysis has shown that intergenic splicing is also possible [1, 2]. Gene pairs such as TNFSF12-TNFSF13 [3], Kua-UBE2V1 [4], and NME1-NME2 [2] are examples reported to have intergenic splicing. It has been suggested that 4-5% of the resulting fused RNA or transcription-induced chimaeras could encode for chimaeric protein sequences and thus increase proteome complexity in the human genome [2]. Splice variants of NME1 and NME2 have been reported and have also shown to be co-transcribed. NME1 and NME2 form the subunits of the Nucleoside diphosphate kinase (NDK) hexamer. This gene, which is also known as NM23, has been linked to tumour metastasis [5].

In this example, SynaMap was used to rapidly map NME1, NME2 and NME1-NME2 genes to locate their positions within the human genome. Representative transcript variants of NME1 (NM_198175.1), NME2 (NM_198175.1) and NME1-NME2 (NM_00101836.1) were mapped to the human genome. SynaMap enables fast and easy mapping and analysis of splice variants on genomes.
To run the example above, please:
  1. Go to
  2. Click on SynaMap.
  3. Click on Test Sequence and select Application Note test sequence NME1 by clicking on the "copy" button next to it.
  4. Click on MAP.
  5. Repeat steps 4 and 5 with Application Note test sequence NME2 and Application Note test sequence NME1- NME2.
Figure 1: The input page of SynaMap showing the sequence in the query box.
Figure 2: SynaMap showing the position of NME1 on human chromosome 17.
Figure 3: SynaMap showing the position of NME2 on human chromosome 17.
Figure 4: SynaMap showing the position of NME1-NME2 on human chromosome 17.
Figure 5: NCBI Map viewer of the genes identified.
Akiva, P, Toporik, A., Edelheit, S., Peretz, Y., Diber, Y., Shemesh, R., Novik, A., and Sorek, Rotem. (2006) Transcription-mediated gene fusion in the human genome. Genome Res. 16:30-36.
Parra, G., Reymod, Alex., Dabbouseh, N., Dermitzakis, E.T., Castelo, R., Thomson, T.M., Antonarakis, S.E., and Guigo, R. (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res. 16:30-36.
Pradet-Balade, B., Medema, J.P., Lopez-Fraga, M., Lorano, J.C., Kolfschoten, G.M., Picard, A., Martinez, A.C., Gracia-Sanz, J.A. and Hahne, M. (2002) An endogenous hybrid mRNA encodes TWE-PRIL, a functional cell surface TWEAK-APRIL fusion protein. EMBO J. 21:5711-5720.
Thomson, T.M., Lozano, J.J, Loukili, N., Carrio, R., Serras, F., Cormand, B., Valeri, M., Diaz, V.M., Abil, J., Burset, M. (2000) Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 10:1743-1756.
Roymas D, Willems R, Van Blockstaele DR, Slegers (2002) Nucleoside diphosphate kinase (NDPK/NM23) and the waltz with multiple partners: possible consequences in tumor metastasis. Clin Exp Metastasis. 19(6): 465-476.

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