Mapping of the Riken full length cDNAs on the mouse chromosomes

In this note, we explain our method of making synteny map of the Riken full length cDNAs on mouse chromosomes.

The construction of the synteny map consists of two steps. The first step is mapping of the Riken full length cDNAs on the human genome draft sequences by sequence homology. The second step is to convert their positions on the human genome to the position on the mouse chromosomes using the known human–mouse homology relations.

For the first step, we used the results of mapping of the Riken full length cDNAs on the human genome by Kondo, Saito et. al. They used the human draft sequences assembled at UCSC and the human finished sequences for Chr21 and 22.

For the second step, we divided it to three sub-steps. They are the identification of the positions of known human genes, the establishment of synteny relations (orthologs) and the mapping of the Riken cDNAs on the mouse chromosomes.

Methods:

1) The identification of the positions of known human genes

We ran e-PCR program with human STS database of NCBI (human.sts) on the human draft sequence. Using another NCBI data (hs_mrna.epcr) that relates STSs to known human genes, we identified the positions of the known human genes on the human genome sequence.

Human genome sequence – (e-PCR) – STS database – (e-PCR) – known human gene

2) The establishment of synteny relations

We used Jackson Lab. human–mouse homology data to make relation between the known human genes and known mouse genes. In the human–mouse homology data, chromosome number and position information (in cM) are also available.

By the procedures of 1) and 2), the positions of 956 known genes on the human genome were mapped on the mouse chromosomes.

3) The mapping of the Riken cDNAs on the mouse chromosomes

To map one of the Riken cDNAs to the mouse chromosomes, we used two pairs of the human–mouse homologous genes that sandwich the Riken cDNA on the human genome. The result of the synteny map is a region on a mouse chromosome specified by the two mouse genes for each Riken cDNA. On the figure of the mouse chromosomes, the center positions of the regions are presented. ( The size of the region of Synteny map is 4 cM on average. The maximum size is 73 cM.)

If the two mouse genes of the pairs of the human–mouse homologous genes are on different mouse chromosomes then the Riken cDNA is not mapped on the mouse chromosomes in the figure.