i have added restriction sites ECO and XHO1. i have tried through all ways using different primers and softwares. what wll be the possible problems associated with it?
you did not mention, the sequence you use for primer designing is public domain database. If so, one of the chance that the research materials you are using is the mutant of that particular gene. The data base sequence might be the WT version or the vice-versa.
Sometimes if the sequence is GC rich it can form a loop with a high GC region at the neck of the loop and an enzyme can read across the loop making a shorter amplimer. Try pcr with DMSO up to 8% or in final concentration of 1M betaine to minimise secondary structure problems, Also BLAST your primers in case they anneal to another region and the smaller amplimer is just amplifying better. What size marker is that picture....the amplimer looks much smaller than 500 to me
In this picture , the product size is around 200 bp. As Paul suggested that BLAST your primers to check the annealing of the primers. Otherwise redesign the primers and analyse primers for hairpin loop and others features.
What size are the bands in your DNA ladder? Double-check that you aren't off with your size estimate.
Other possibilities:
You are amplifying a different region than you thought. As others said, BLAST your primers to see if they could anneal to another gene.
Are you using the same strain/variety/ecotype of organism to design primers and set up PCR? There are often differences between the reference genome and close relatives. The gene might be different lengths in different organisms. You could sequence to find out.
Did you use cDNA or gDNA as your starting material? If you used cDNA, you might have removed a very tiny intron (unlikely but possible)
Double check if your DNA ladder isn't missing the smallest product? Sometimes in old ladders, the smallest product is barely visible and you may count the second product as the first and thus being off by 100 basepairs