primer sequence - reverse primer sequence (Oct/19/2008 )

Hi,
I have the following reverse primer sequence: gccatgatctgcaccacgttacctttcttttcctccaacgcccc. I have tried the NCBI Blast tool to map the sequence and it shows the following hits NM 007912.4 and NM 207655.2 mRNA. My problem is that I cannot find where the sequence for this reverse primer is on the transcript. Can anyone help?

Thanks,

sybr

Blasting your sequence shows many hits to mouse EGFR, with bases 19-44. Here's some sample output, a few of very many hits:
>dbj|AK014017.1| UniGene infoGeoGene info Mus musculus 13 days embryo head cDNA, RIKEN full-length enriched
library, clone:3110007E23 product:EPIDERMAL GROWTH FACTOR
RECEPTOR (FRAGMENT) homolog [Mus musculus], full insert sequence
Length=1053

GENE ID: 13649 Egfr | epidermal growth factor receptor [Mus musculus]
(Over 100 PubMed links)

Score = 52.0 bits (26), Expect = 1e-04
Identities = 26/26 (100%), Gaps = 0/26 (0%)
Strand=Plus/Minus

Query 19 TTACCTTTCTTTTCCTCCAACGCCCC 44
||||||||||||||||||||||||||
Sbjct 342 TTACCTTTCTTTTCCTCCAACGCCCC 317


>dbj|AK049452.1| UniGene infoGeoGene info Mus musculus 7 days embryo whole body cDNA, RIKEN full-length
enriched library, clone:C430014G08 product:unclassifiable,
full insert sequence
Length=3481

GENE ID: 13649 Egfr | epidermal growth factor receptor [Mus musculus]
(Over 100 PubMed links)

Score = 52.0 bits (26), Expect = 1e-04
Identities = 26/26 (100%), Gaps = 0/26 (0%)
Strand=Plus/Minus

Query 19 TTACCTTTCTTTTCCTCCAACGCCCC 44
||||||||||||||||||||||||||
Sbjct 234 TTACCTTTCTTTTCCTCCAACGCCCC 209


>gb|AF456454.1|AF456454 Gene info Mus musculus epidermal growth factor receptor (Egfr) gene, exon
1 and partial cds
Length=1498

GENE ID: 13649 Egfr | epidermal growth factor receptor [Mus musculus]
(Over 100 PubMed links)

Score = 52.0 bits (26), Expect = 1e-04
Identities = 26/26 (100%), Gaps = 0/26 (0%)
Strand=Plus/Minus

Query 19 TTACCTTTCTTTTCCTCCAACGCCCC 44
||||||||||||||||||||||||||
Sbjct 623 TTACCTTTCTTTTCCTCCAACGCCCC 598


>emb|BX255277.5| Download subject sequence spanning the HSP Mouse DNA sequence from clone RP23-478B14 on chromosome 11, complete
sequence
Length=169765

Score = 52.0 bits (26), Expect = 1e-04
Identities = 26/26 (100%), Gaps = 0/26 (0%)
Strand=Plus/Minus

Query 19 TTACCTTTCTTTTCCTCCAACGCCCC 44
||||||||||||||||||||||||||
Sbjct 121068 TTACCTTTCTTTTCCTCCAACGCCCC 121043

Thanks. I get the same hits, but when I try and find that same primer sequence in the mouse EGFR transcript i can't see where it matches, ie, which exon? is it closer to the 5' or 3' of that sequence?

Thanks

if you look at this hit:
>gb|AF456454.1|AF456454 Gene info Mus musculus epidermal growth factor receptor (Egfr) gene, exon
1 and partial cds
Length=1498

GENE ID: 13649 Egfr | epidermal growth factor receptor [Mus musculus]
(Over 100 PubMed links)

Score = 52.0 bits (26), Expect = 1e-04
Identities = 26/26 (100%), Gaps = 0/26 (0%)
Strand=Plus/Minus

Query 19 TTACCTTTCTTTTCCTCCAACGCCCC 44
||||||||||||||||||||||||||
Sbjct 623 TTACCTTTCTTTTCCTCCAACGCCCC 598

it is teling you that the hit is located within the sequence AF456454 between bases 598 and 623. You are probably missing it because it will appear as a reverse complement (note the order of the numbers in the hit).