Sonic hedgehog (SHH), Desert hedgehog (DHH) and Indian hedgehog (IHH) bind to 
Patched family receptors (PTCH1 and PTCH2) to transduce signals to GLI1, GLI2 
and GLI3. GLI family transcription factors then activate transcription of 
Hedgehog target genes, such as FOXE1 and FOXM1 encoding Forkhead-box 
transcription factors. Hedgehog signaling pathway plays a pivotal role in a 
variety of human tumors, such as gastric cancer, pancreatic cancer, colorectal 
cancer, breast cancer, prostate cancer, basal cell carcinoma and brain tumors. 
Rat orthologs for human DHH and IHH remain to be identified. Here, we identified 
and characterized rat Dhh and Ihh genes by using bioinformatics. Rat Dhh 
complete coding sequence (CDS) was determined by assembling nucleotide positions 
426397-426963, 429715-429976 and 430244-430898 of the AC114446.3 genome 
sequence. Rat Ihh complete CDS was determined by assembling nucleotide positions 
63433-64033, 66432-66693 and 68242-69169 of AC095777.6 genome sequence. Rat Dhh 
mRNA was expressed in prostate, duodenum and dorsal root ganglia, while rat Ihh 
mRNA was expressed in cartilage. Rat Dhh showed 99.7% total-amino-acid identity 
with mouse Dhh, and 96.5% total-amino-acid identity with human DHH. Rat Ihh and 
human IHH were shorter than mouse Ihh by 38 amino acids. Rat Ihh showed 97.6% 
total-amino-acid identity with mouse Ihh and 94.4% total-amino-acid identity 
with human IHH. Hedgehog family proteins consist of signal peptide, Hedgehog 
ligand peptide and C-terminal peptide. Hedgehog ligand peptides derived from 
mammalian Hedgehog family proteins were conserved well, while C-terminal 
peptides were relatively divergent. The HPLGMXXXXS motif in the C-terminus was 
conserved in Shh orthologs and Ihh orthologs, but not in Dhh orthologs.