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!!!
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Sbjct 1996 GATACAGATACAGA 2009
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???