Assuming that this gene is 'conserved' or 'partially conserved' across different organisms, then you can design PCR primers based on the conserved regions or design 'degenerate' primers (as mentioned by Biswapriya) from the partially conserved regions to amplify out the gene of your organism (invert PCR might be needed for the rest outward part of the gene, if you only amplify part of the gene). However, if this gene sequence is very diverse across different organisms, then these approaches will become difficult...........

Easy. You need to design "degenerate PCR Primers" based on sequence alignment of the mRNA sequences from all organism known in GenBank etc.. It worked for me everytime as well. Depending on how well conserved the gene is across taxa (within plants or plants vs animals and also say fishes vs frogs) chances are that too much "redundancy in sequences" can amplify junk. But with some optimization using a gradient PCR machine, these primers can work wonderfully. Check the degeneracy of the N-and C-terminal of the protein sequences first across all these known sequences, and then go to nucleotide levels to generate these primers. One example resource would be here: http://medicine.yale.edu/lab/koelle/protocols/745_180567_DegeneratePCR.pdf. Make sure to use Inosine (I) instead of using all 4-fold degeneracy say (A/T/G/C) for one-nucleotide position. The rationale is to reduce the fold-degeneracy as well as to achieve specificity enough. Also, you may prefer to group the sequences to "more conserved list" and thus design 2-3 or more numbers of such degenerate PCR primers. Alternatively, you can try out using oligo(dT)18 primers (that complements poly-AAAA Tails in mRNA) for the reverse primer and use those sets of degenerate PCR primers based on "N-terminal" ends of those proteins/ sequences as "forward" primer. These would work across taxa with variable size amplicons from each species ! Hope it helps. Thanks, Biswa

Answers are :degenerate PCR primers. The forward degenerate PCR primers needs to be designed manually looking at the aligned nucleotide sequences of the  homologous sequences as submitted in NCBI-GenBank or similar public resources. So if degenerate forward primers based on conserved residues at N-terminal ends of the proteins and oligo(dT)18 reverse primers that are complimentary to the poly-AA Tails in mRMA, then one can get amplicons of varied lengths for different organisms. A little twitching of the PCR conditions using a few gradient PCR experiments would help you amplify much species-specific gene of interest. Also try to use I (Inosine) as a base for positions with 4-fold degeneracy such as A/T/G/C; while grouping the nucleotide sequences (end to end) using Clustal W or any such free multiple sequence alignment tool, would allow you to group the sequences and thus "design several such degenerate PCR primers" to use them taxa-wise (say within plants, or across 2 families in animals, or across several families of plants/ animals). Just order to synthesize more amounts, as with growing fold of degeneracy, the combination of primer mixes yields would be differential ! This approach worked for me zillion times !

Many useful links are there on the web: http://dps.plants.ox.ac.uk/langdalelab/protocols/PCR/degenerate_PCR.pdf and so on. Let me know if you need further details or clarifications.  Best wishes.

I would suggest trying "inverse PCR". This means you start with digested genomic DNA and ligate those fragments to generate circulat molecules (try different enzymes to find the one that is best suited in terms of circle-size). Then you use primers that are facing "outwards" on the already known sequence region. Upon amplification, you are elongating the 5' as well as the 3' ragion starting from the core sequence. This should help you to generate ever more of the neighbouring sequences.

Hope that helps, best regards, Christian

Assuming that this gene is 'conserved' or 'partially conserved' across different organisms, then you can design PCR primers based on the conserved regions or design 'degenerate' primers (as mentioned by Biswapriya) from the partially conserved regions to amplify out the gene of your organism (invert PCR might be needed for the rest outward part of the gene, if you only amplify part of the gene). However, if this gene sequence is very diverse across different organisms, then these approaches will become difficult...........

Thanks for the help Biswapriya, Christian and Yuan-Yeu!