Degenerate primer design for DIG in situ hybridization
If the gene is supposed to be well conserved then you can use the sequence from the related species. 

For protein coding genes target the ISH probe to the coding region which is more likely to be conserved. 

What you can also do subsequently is to:


amplify the CDS
do 3' and 5' RACE
Clone in a plasmid (do a blunt end or TA cloning)
Sequence the insert
Design exact primers



  are there any other good databases for gene sequences?


EMBL and DDBJ