Hi Bhagya..Enhancers have the roles in gene regulations by binding to the transcription start sites. It might be located several 1000 bps away from TSS. Prediction of gene just depends on the ORF found in the genome. Its regulation is altogether a different aspect. A gene might be up/down regulated or totally turned off due to enhancers functions. Thanks!

actually, in some cases we are using the knowledge on regulators for better prediction of exact function of the gene/operone. I am not sure this can be done automatically in general (look previous comment), but in some cases it could be done and of course this is one of the approaches for manual functional annotation. You can search for papers of D. Rodionov, he is a specialist in regulation. There are also several regulators databases, eg. Regprecise http://regprecise.lbl.gov/RegPrecise/ which can help you to predict some known regulators.  Hope, it`ll help you

You probably know, but enhancers seem to be a way to more finely tune expression of a gene, in terms of location or timing. A ubiquitously expressed gene (ie housekeeping) is less likely to make use of enhancers than a tissue-specific gene (ie transcription factor for limb development). At least that's the trend; the genome is big and there are probably exceptions. As part of the (mod)/ENCODE projects, likely regulatory elements were predicted through the presence of specific epigenetic modifications and transcription factor binding events and the mouse/human genome was parsed into functional domains.

Some of the gene prediction programs take into account the promoter consensus sequences and CpG islands ....but not enhancers themselves.

Absolutely No.. Enhancers are not next to gene itself. they are very far away. so this cant be helpful in predicting genes. 

Thank you all.

            Thank you Ilya V Kublanov, information about regulators databases helped me.