Design of in-situ probes for closely-related genes

We are trying to study the expression pattern during ZF development of
3 members of a gene family that shows a high degree of nucleotide
sequence identity within the coding region.
We obtained some preliminary results (mainly uniform and ubiquitous
expression) with 400-600 bp probes designed in the more divergent 3'
UTR, now we would like to confirm the data with a second set of probes
designed on a different portion of the transcript.

Considering the limited size of the 5' UTR, what is the minimum length
recommended for whole mount in situ hybridization probes?

As an alternative we could use probes designed within the coding
region: is it possible to avoid cross-hybridization with sequences
75-80% identical working at high stringency conditions?

Thanks

Giuseppe Borsani

Department of Biomedical Sciences and Biotechnology
School of Medicine
University of Brescia
Viale Europa 11
25123 - Brescia, Italy

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