You can try to paste it here (Safari browser not supported):

http://supfam.cs.bris.ac.uk/SUPERFAMILY/hmm.html

Select 6-frame translation if you do not have a protein model. This may give you some idea as to its function (and structure) if BLAST doesn't help you.

@Julian: Tons of thanks for your valuable suggestion, i did it immediately and got some results, perhaps useful for me..but i am not sure, so could you drive me more ??? what i did actually....i pasted my nucleotide sequence, selection with 'Nucleotide both strands (6)' and got results such as:

1. Sorry No Significant Hits. :'(

2. Ambiguous hits for 2 and suggested 2 kind of pdb that have 95% similarity.

So is this really make any sense ????

What Superfamily actually does is translating your sequence into the six possible open reading frames and scan for conserved functional domains. You can achieve the same result using Interproscan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) with your predicted protein (try to visually identify the correct ORF using this http://web.expasy.org/translate/). The presence of conserved domains can usually give you some information about the possible function/structure of a protein even when you don't find any obvious BLAST similarity.

Instead of searching/blasting RefSeq, you should simply do "blastn", searching all nucleotides including genomic DNA, mRNA, EST, etc. A RefSeq was only created when there are sufficient transcripts to support a full-length mRNA and/or some functional and homology data to support the existence of such a gene. There are many gene loci that do not have a RefSeq due to incompleteness of available data for creating a full-length gene. From Blastn, if you find some hits, you may be able to get a hint on if you indeed have a real transcript and what it might be based on what the hits are.

I would not directly search for ORFs because NGS reads are usually error-prone and the errors can cause frameshift and premature stop codons. Moreover, your gene could be a non-coding RNA and you will not find any protein similarity.

Novel gene of which specie /class/order (animal/plant etc)? specifying this would make it easier to give you a better solution.

@Amir: For Human RNA-seq

@ Xuejun Chen : Thank you sir for your nice explanation, i did it already in both medium (by direct nucleotide and after translating ORF)..in both cases, fortunately i found same nucleotide and protein hits so i hope i am in right way.......could you suggest me , what i can do more with gene ?? In order to validate & confirm it ..

tons of thanks for your time & words..

You can see what the protein hit is and if the protein hit has a function description. This will help you determine what function your gene may have, which should be similar to the protein hit. Do can also determine if other mRNA or EST hits from human align nearly perfectly with your gene. If yes, you can be sure your gene is indeed expressed and is real.

I'll tell you another website to blast human genome: the UCSC genome blat

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

paste your seq in and search. Pick the highest score hit to view. In the genome viewer, see if there is any gene defined in the aligned region, and check if there are many transcripts aligned to that region. You can even load in transcripts from other species to find homology support.