


Investigating Intergenic Splice Forms Using SynaMap™

Description:
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:

Go to www.mgrc.com.my.
Click on SynaMap.
Click on Test Sequence and select Application Note test sequence NME1 by clicking on the "copy" button next to it.
Click on MAP.
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.

References:
1.	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.
2.	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.
3.	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.
4.	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.
5.	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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