Hi everybody,

I am designing primer for insulin receptor and when I sent primer to blast, blast is giving two differnt results.

According to balst results:
1-Reference assemly: my primer exatcly matches to insulin receptor intron region that I will expect
Homo sapiens chromosome 19 genomic contig, reference assembly
Length=7286004

Features in this part of subject sequence:
insulin receptor

Score = 48.1 bits (24), Expect = 1e-04
Identities = 24/24 (100%), Gaps = 0/24 (0%)
Strand=Plus/Plus

Query 1 TACGCGATGCAGGAGCTACCGTCC 24
||||||||||||||||||||||||
Sbjct 7233656 TACGCGATGCAGGAGCTACCGTCC 7233679



2- alternate assembly
(based on Celera assembly) My primer exactly mathes to insulin receptor intron region and mathes to exactly to another gene

Features flanking this part of subject sequence:
25805 bp at 5' side: insulin receptor
[b]145327 bp at 3' side: Rho-specific guanine nucleotide exchange factor p114[/b]


Score = 48.1 bits (24), Expect = 1e-04
Identities = 24/24 (100%), Gaps = 0/24 (0%)
Strand=Plus/Plus

Query 1 TACGCGATGCAGGAGCTACCGTCC 24
||||||||||||||||||||||||
Sbjct 6489783 TACGCGATGCAGGAGCTACCGTCC 6489806


I do not know which one I can belive refernce assembly results or celera assembly result.

Could you please give advise for this circumtances?

Thank you for cooperatin

Arman

This sounds perhaps like an annotation difference, rather than a sequence difference. Both are near the insulin receptor gene. Given a choice, I'd believe the reference sequence.