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shRNA negative control - (Dec/02/2009 )

Hi everyone!!

Could you help me with knowing if this sequence (GGATACAGATACAGATACAA) ca be used as a good negative control for shRNA experiments in mouse???
Thank you!!!

-yarince-

This control is not very good but still usable because it has significant homology with other mRNA sequences. Below are the BLAST results against mouse refSeq.

ref|NM_019658.5| UniGene infoGeoGene info Mus musculus soc-2 (suppressor of clear) homolog (C. elegans)
(Shoc2), mRNA
Length=3964

GENE ID: 56392 Shoc2 | soc-2 (suppressor of clear) homolog (C. elegans)
[Mus musculus] (Over 10 PubMed links)

Score = 30.1 bits (32), Expect = 0.24
Identities = 16/16 (100%), Gaps = 0/16 (0%)
Strand=Plus/Minus

Query 2 GATACAGATACAGATA 17
||||||||||||||||
Sbjct 2180 GATACAGATACAGATA 2165


Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 5 ACAGATACAGATACA 19
|||||||||||||||
Sbjct 2183 ACAGATACAGATACA 2169


>ref|NM_145436.2| UniGene infoGeoGene info Mus musculus cell division cycle 27 homolog (S. cerevisiae) (Cdc27),
mRNA
Length=5783

GENE ID: 217232 Cdc27 | cell division cycle 27 homolog (S. cerevisiae)
[Mus musculus] (Over 10 PubMed links)

Score = 30.1 bits (32), Expect = 0.24
Identities = 18/19 (94%), Gaps = 0/19 (0%)
Strand=Plus/Plus

Query 1 GGATACAGATACAGATACA 19
||| |||||||||||||||
Sbjct 4992 GGACACAGATACAGATACA 5010


>ref|NM_001043355.2| UniGene infoGene info Mus musculus microtubule-associated protein 6 (Mtap6), transcript
variant 3, mRNA
Length=2335

GENE ID: 17760 Mtap6 | microtubule-associated protein 6 [Mus musculus]
(Over 10 PubMed links)

Score = 30.1 bits (32), Expect = 0.24
Identities = 18/19 (94%), Gaps = 0/19 (0%)
Strand=Plus/Plus

Query 2 GATACAGATACAGATACAA 20
||||||| |||||||||||
Sbjct 1796 GATACAGGTACAGATACAA 1814


>ref|NM_010837.3| UniGene infoGeoGene info Mus musculus microtubule-associated protein 6 (Mtap6), transcript
variant 1, mRNA
Length=3447

GENE ID: 17760 Mtap6 | microtubule-associated protein 6 [Mus musculus]
(Over 10 PubMed links)

Score = 30.1 bits (32), Expect = 0.24
Identities = 18/19 (94%), Gaps = 0/19 (0%)
Strand=Plus/Plus

Query 2 GATACAGATACAGATACAA 20
||||||| |||||||||||
Sbjct 2892 GATACAGGTACAGATACAA 2910


>ref|NM_001163333.1| UniGene infoGene info Mus musculus CTTNBP2 N-terminal like (Cttnbp2nl), transcript
variant 3, mRNA
Length=4830

GENE ID: 80281 Cttnbp2nl | CTTNBP2 N-terminal like [Mus musculus]
(Over 10 PubMed links)

Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 3 ATACAGATACAGATA 17
|||||||||||||||
Sbjct 3076 ATACAGATACAGATA 3062


>ref|NM_001163332.1| UniGene infoGene info Mus musculus CTTNBP2 N-terminal like (Cttnbp2nl), transcript
variant 2, mRNA
Length=4838

GENE ID: 80281 Cttnbp2nl | CTTNBP2 N-terminal like [Mus musculus]
(Over 10 PubMed links)

Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 3 ATACAGATACAGATA 17
|||||||||||||||
Sbjct 3084 ATACAGATACAGATA 3070


>ref|NM_030249.4| UniGene infoGene info Mus musculus CTTNBP2 N-terminal like (Cttnbp2nl), transcript
variant 1, mRNA
Length=4946

GENE ID: 80281 Cttnbp2nl | CTTNBP2 N-terminal like [Mus musculus]
(Over 10 PubMed links)

Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 3 ATACAGATACAGATA 17
|||||||||||||||
Sbjct 3192 ATACAGATACAGATA 3178


>ref|NM_026605.2| UniGene infoGene info Mus musculus symplekin (Sympk), mRNA
Length=4121

GENE ID: 68188 Sympk | symplekin [Mus musculus] (Over 10 PubMed links)

Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 6 CAGATACAGATACAA 20
|||||||||||||||
Sbjct 2534 CAGATACAGATACAA 2520


>ref|NM_001033380.3| UniGene infoGeoGene info Mus musculus inositol 1,4,5-triphosphate receptor interacting
protein-like 2 (Itpripl2), mRNA
Length=6891

GENE ID: 319622 Itpripl2 | inositol 1,4,5-triphosphate receptor interacting
protein-like 2 [Mus musculus] (10 or fewer PubMed links)

Score = 28.3 bits (30), Expect = 0.85
Identities = 15/15 (100%), Gaps = 0/15 (0%)
Strand=Plus/Minus

Query 5 ACAGATACAGATACA 19
|||||||||||||||
Sbjct 4165 ACAGATACAGATACA 4151


>ref|NR_003549.1| Gene infoDownload subject sequence spanning the HSP Mus musculus RIKEN cDNA 3110048L19 gene (3110048L19Rik), non-coding
RNA
Length=33831

GENE ID: 73233 3110048L19Rik | zinc finger pseudogene [Mus musculus]
(Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 16/17 (94%), Gaps = 0/17 (0%)
Strand=Plus/Minus

Query 2 GATACAGATACAGATAC 18
|| ||||||||||||||
Sbjct 10503 GAGACAGATACAGATAC 10487


>ref|NM_022814.2| UniGene infoGeoGene infoDownload subject sequence spanning the HSP Mus musculus sushi, von Willebrand factor type A, EGF and pentraxin
domain containing 1 (Svep1), mRNA
Length=11275

GENE ID: 64817 Svep1 | sushi, von Willebrand factor type A, EGF and pentraxin
domain containing 1 [Mus musculus] (Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 17/19 (89%), Gaps = 0/19 (0%)
Strand=Plus/Plus

Query 1 GGATACAGATACAGATACA 19
|||| | ||||||||||||
Sbjct 9670 GGATTCGGATACAGATACA 9688


>ref|NM_009390.2| UniGene infoGeoGene info Mus musculus tolloid-like (Tll1), mRNA
Length=4928

GENE ID: 21892 Tll1 | tolloid-like [Mus musculus] (Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Minus

Query 7 AGATACAGATACAA 20
||||||||||||||
Sbjct 4336 AGATACAGATACAA 4323


>ref|NM_130877.2| UniGene infoGeoGene info Mus musculus paternally expressed 10 (Peg10), transcript variant
1, mRNA
Length=6677

GENE ID: 170676 Peg10 | paternally expressed 10 [Mus musculus]
(Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 16/17 (94%), Gaps = 0/17 (0%)
Strand=Plus/Minus

Query 2 GATACAGATACAGATAC 18
||||| |||||||||||
Sbjct 2341 GATACTGATACAGATAC 2325


>ref|NM_001040611.1| UniGene infoGeoGene info Mus musculus paternally expressed 10 (Peg10), transcript variant
1, mRNA
Length=6677

GENE ID: 170676 Peg10 | paternally expressed 10 [Mus musculus]
(Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 16/17 (94%), Gaps = 0/17 (0%)
Strand=Plus/Minus

Query 2 GATACAGATACAGATAC 18
||||| |||||||||||
Sbjct 2341 GATACTGATACAGATAC 2325


>ref|NM_178045.3| UniGene infoGeoGene info Mus musculus Ras association (RalGDS/AF-6) domain family member
4 (Rassf4), mRNA
Length=6325

GENE ID: 213391 Rassf4 | Ras association (RalGDS/AF-6) domain family member 4
[Mus musculus] (Over 10 PubMed links)

Score = 26.5 bits (28), Expect = 3.0
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Plus

Query 2 GATACAGATACAGA 15
||||||||||||||
Sbjct 1996 GATACAGATACAGA 2009

-pcrman-

Thank you very much!

Then, How could I design a good negative control for mouse?? Do you know some database where I could find it???

-yarince-