From Tol2Kit
(→att site shared sequences) |
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| + | 12-09-07 Minor edits to fix a couple of sequences and clarify names (especially the attBXX_primer sequences). | ||
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== att site shared sequences == | == att site shared sequences == | ||
Here is a set of "shared" sequences--the core stretch that is shared between attB/P/L/R for att1-4. These are useful for stitching together entry and destination sequences to calculate the sequence of a final expression clone. | Here is a set of "shared" sequences--the core stretch that is shared between attB/P/L/R for att1-4. These are useful for stitching together entry and destination sequences to calculate the sequence of a final expression clone. | ||
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== list of att sites == | == list of att sites == | ||
| − | Below are all of the att sequences (attB, P, L, and R) used in the original three-part multisite Gateway system. These sequences come from the Invitrogen documentation, and we have seen a few single-base differences from the actual sequences of our clones (it's unclear whether these are documentation mistakes or mutations that have accumulated over time). | + | Below are all of the att sequences (attB, P, L, and R) used in the original three-part multisite Gateway system. These sequences come from the Invitrogen documentation, and we have seen a few single-base differences from the actual sequences of our clones (it's unclear whether these are documentation mistakes or mutations that have accumulated over time). Some of these differences are indicated by degenerate IUPAC codes in the sequences below. |
| + | |||
| + | The _primer sequences are for use in designing att PCR primers. Note that we use the nomenclature of the Invitrogen [[Invitrogen manual | Version D manual]] (3/7/07), not later versions. | ||
<pre> | <pre> | ||
| − | > | + | >attB1_primer |
GGGGACAAGTTTGTACAAAAAAGCAGGCT | GGGGACAAGTTTGTACAAAAAAGCAGGCT | ||
| − | > | + | >attB1R_primer |
GGGGACTGCTTTTTTGTACAAACTTG | GGGGACTGCTTTTTTGTACAAACTTG | ||
| − | > | + | >attB2_primer |
GGGGACAGCTTTCTTGTACAAAGTGG | GGGGACAGCTTTCTTGTACAAAGTGG | ||
| − | > | + | >attB2R_primer |
GGGGACCACTTTGTACAAGAAAGCTGGGT | GGGGACCACTTTGTACAAGAAAGCTGGGT | ||
| − | > | + | >attB3R_primer |
GGGGACAACTTTGTATAATAAAGTTG | GGGGACAACTTTGTATAATAAAGTTG | ||
| + | >attB4_primer | ||
| + | GGGGACAACTTTGTATAGAAAAGTTG | ||
| + | |||
| + | >attB1 | ||
| + | CAAGTTTGTACAAAAAAGCAGGCT | ||
| + | >attB2 | ||
| + | ACCCAGCTTTCTTGTACAAAGTGG | ||
| + | >attB3 | ||
| + | CAACTTTGTATAATAAAGTTG | ||
>attB4 | >attB4 | ||
| − | + | CAACTTTGTATAGAAAAGTTG | |
| + | |||
>attL1 | >attL1 | ||
CAAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACAT | CAAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACAT | ||
| Line 41: | Line 55: | ||
AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATT | AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATT | ||
GATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAAAGTTG | GATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAAAGTTG | ||
| + | |||
>attP1 | >attP1 | ||
AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACATT | AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACATT | ||
| Line 77: | Line 92: | ||
AAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGA | AAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGA | ||
ATCAACTACTTAGATGGTATTAGTGACCTGTA | ATCAACTACTTAGATGGTATTAGTGACCTGTA | ||
| + | |||
>attR1 | >attR1 | ||
CAAGTTTGTACAAAAAAGTTGAACGAGAAACGTAAAATGATATAAATATC | CAAGTTTGTACAAAAAAGTTGAACGAGAAACGTAAAATGATATAAATATC | ||
| Line 83: | Line 99: | ||
ACCTGTA | ACCTGTA | ||
>attR2 | >attR2 | ||
| − | + | TACAGGTCACTAATACCATCTAAGTAGTTGRTTCATAGTGACTGCATATG | |
TTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTA | TTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTA | ||
ATATATTGATATTTATATCATTTTACGTTTCTCGTTCAACTTTCTTGTAC | ATATATTGATATTTATATCATTTTACGTTTCTCGTTCAACTTTCTTGTAC | ||
Revision as of 00:34, 10 December 2007
12-09-07 Minor edits to fix a couple of sequences and clarify names (especially the attBXX_primer sequences).
Here is a set of "shared" sequences--the core stretch that is shared between attB/P/L/R for att1-4. These are useful for stitching together entry and destination sequences to calculate the sequence of a final expression clone.
>att1_shared TTTGTACAAAAAAG >att2_shared CTTTCTTGTACAAAGT >att3_shared CAACTTTATTATACA >att4_shared CAACTTTGTATAGAAAAGTTG
list of att sites
Below are all of the att sequences (attB, P, L, and R) used in the original three-part multisite Gateway system. These sequences come from the Invitrogen documentation, and we have seen a few single-base differences from the actual sequences of our clones (it's unclear whether these are documentation mistakes or mutations that have accumulated over time). Some of these differences are indicated by degenerate IUPAC codes in the sequences below.
The _primer sequences are for use in designing att PCR primers. Note that we use the nomenclature of the Invitrogen Version D manual (3/7/07), not later versions.
>attB1_primer GGGGACAAGTTTGTACAAAAAAGCAGGCT >attB1R_primer GGGGACTGCTTTTTTGTACAAACTTG >attB2_primer GGGGACAGCTTTCTTGTACAAAGTGG >attB2R_primer GGGGACCACTTTGTACAAGAAAGCTGGGT >attB3R_primer GGGGACAACTTTGTATAATAAAGTTG >attB4_primer GGGGACAACTTTGTATAGAAAAGTTG >attB1 CAAGTTTGTACAAAAAAGCAGGCT >attB2 ACCCAGCTTTCTTGTACAAAGTGG >attB3 CAACTTTGTATAATAAAGTTG >attB4 CAACTTTGTATAGAAAAGTTG >attL1 CAAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACAT TGATGAGCAATGCTTTTTTATAATGCCAACTTTGTACAAAAAAGCAGGCT >attL2 ACCCAGCTTTCTTGTACAAAGTTGGCATTATAAGAAAGCATTGCTTATCA ATTTGTTGCAACGAACAGGTCACTATCAGTCAAAATAAAATCATTATTTG >attL3 CAACTTTATTATACAAAGTTGGCATTATAAAAAAGCATTGCTTATCAATT TGTTGCAACGAACAGGTCACTATCAGTCAAAATAAAATCATTATTT >attL4 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATT GATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAAAGTTG >attP1 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACACATT GATGAGCAATGCTTTTTTATAATGCCAACTTTGTACAAAAAAGCTGAACG AGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATA AAAAACAGACTACATAATACTGTAAAACACAACATATCCAGTCACTATGA ATCAACTACTTAGATGGTATTAGTGACCTGTA >attP1R AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATT GATAAGCAATGCTTTTTTATAATGCCAACTTTGTACAAAAAAGTTGAACG AGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATA AAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGA ATCAACTACTTAGATGGTATTAGTGACCTGTA >attP2 AATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATTG ATAAGCAATGCTTTCTTATAATGCCAACTTTGTACAAGAAAGCTGAACGA GAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAA AAAACAGACTACATAATACTGTAAAACACAACATATCCAGTCACTATGAA TCAACTACTTAGATGGTATTAGTGACCTGTA >attP2R TACAGGTCACTAATACCATCTAAGTAGTTGATTCATAGTGACTGCATATG TTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTA ATATATTGATATTTATATCATTTTACGTTTCTCGTTCAACTTTCTTGTAC AAAGTTGGCATTATAAAAAAGCATTGCTTATCAATTTGTTGCAACGAACA GGTCACTATCAGTCAAAATAAAATCATTATTT >attP3 TACAGGTCACTAATACCATCTAAGTAGTTGATTCATAGTGACTGCATATG TTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTA ATATATTGATATTTATATCATTTTACGTTTCTCGTTCAACTTTATTATAC AAAGTTGGCATTATAAAAAAGCATTGCTTATCAATTTGTTGCAACGAACA GGTCACTATCAGTCAAAATAAAATCATTATTT >attP4 AAATAATGATTTTATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATT GATAAGCAATGCTTTTTTATAATGCCAACTTTGTATAGAAAAGTTGAACG AGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATA AAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGA ATCAACTACTTAGATGGTATTAGTGACCTGTA >attR1 CAAGTTTGTACAAAAAAGTTGAACGAGAAACGTAAAATGATATAAATATC AATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAA AACACAACATATGCAGTCACTATGAATCAACTACTTAGATGGTATTAGTG ACCTGTA >attR2 TACAGGTCACTAATACCATCTAAGTAGTTGRTTCATAGTGACTGCATATG TTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTA ATATATTGATATTTATATCATTTTACGTTTCTCGTTCAACTTTCTTGTAC AAAGTGG >attR3 CCATAGTGACTGGATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTT TATGCAAAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCT CGTTCAACTTTATTATACATAGTTG >attR4 CAACTTTGTATAGAAAAGTTGAACGAGAAACGTAAAATGATATAAATATC AATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAA AACACAACATATCCAGTCACTATGG