Synthetic Gene DataBase
 

Synthetic Gene 115


 
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Field NameNatural GeneSynthetic Gene
SGDB Gene ID106115
GenBank AccessionAF286224AY181195
GenBank GI1356921737413992
Gene Namegaggag
Gene Length (bp)14851485
Specieshuman Immunodeficiency Virus (HIV-1)Homo sapiens, Mus musculus
Strains96ZM651293T cells, mouse spleen cells
CDSatgggtgcgagagcgtcaatattaagagggggaaaattagataaatgggaaaaaattagg
ctaaggccagggggaaagaaacgctatatgataaaacacctagtatgggcaagcagggag
ctggaaagatttgcgcttaaccctggccttttagaaacatcagaaggctgtaaacaaata
atgaaacagctacaaccagctcttcagacaggaacggaggaacttagatcattatacaac
acagtagcaactctctattgtgtacatgaaggggtagaggtacgagacaccaaggaagcc
ttagacaggatagaggaagaacaaaacaaaattcagcaaaaaatacagcaaaaaacacag
caagcggctgacggaaaggtcagtcaaaattatcctatagtgcagaatctccaagggcaa
atggtacaccagaaactatcacctagaactttgaatgcatgggtaaaagtaatagaagaa
aaagcttttagcccagaggtaatacccatgtttacagcattatcagaaggagccacccca
caagatttaaacaccatgttaaatacagtggggggacatcaagcagccatgcaaatgtta
aaagatactatcaatgaggaggctgcagaatgggatagattacatccagtgcatgcaggg
cctattgcaccaggccaaatgagagaaccaaggggaagtgatatagcaggaactactagt
accctccaagaacagatagcatggatgacaagtaatccccctattccagtgggagacatc
tataaaagatggataattctggggttaaataaaatagtaagaatgtatagccctgtcagc
attttggacataaaacaagggccaaaggaaccctttagagactatgtagaccggttcttc
aaaactttaagagctgaacaggctacacaagaagtaaaaaattggatgacagacaccttg
ttggtccaaaatgcaaacccagattgcaagaccattttaaaagcattaggaccaggggct
acattagaagaaatgatgacagcatgtcaaggagtgggaggacctagccacaaagcaaga
gtgttggctgaggcaatgagccaaacaaatagtgtaaacatactgatgcagaaaagcaat
tttaaaggaaataaaagaatggttaaatgttttaactgtggtaaggaagggcacatagcc
agaaattgcagggcccctaggaaaaagggctgttggaaatgtggaaaggagggacaccaa
atgaaagactgtactgagaggcaggctaattttttagggaaaatttggccttcccacaag
ggaaggccagggaatttccttcagaacaggccagagccaacagccccaccagcagagagc
ttcaggttcgaggagacaacccccgctccgaagcaggagtcgaaagacagggaagcctta
acttccctcaaatcactctttggcagcgaccccttgtctcaataa
atgggcgcccgcgccagcatcctgcgcggcggcaagctggacaagtgggagaagatccgc
ctgcgccccggcggcaagaagcgctacatgatcaagcacctggtgtgggccagccgcgag
ctggagcgcttcgccctgaaccccggcctgctggagaccagcgagggctgcaagcagatc
atgaagcagctgcagcccgccctgcagaccggcaccgaggagctgcgcagcctgtacaac
accgtggccaccctgtactgcgtgcacgagggcgtggaggtgcgcgacaccaaggaggcc
ctggaccgcatcgaggaggagcagaacaagatccagcagaagatccagcagaaaacccag
caggccgccgacggcaaggtgagccagaactaccccatcgtgcagaacctgcagggccag
atggtgcaccagaagctgagcccccgcaccctgaacgcctgggtgaaggtgatcgaggag
aaggccttcagccccgaggtgatccccatgttcaccgccctgagcgagggcgccaccccc
caggacctgaacaccatgctgaacaccgtgggcggccaccaggccgccatgcagatgctg
aaggacaccatcaacgaggaggccgccgagtgggaccgcctgcaccccgtgcacgccggc
cccatcgcccccggccagatgcgcgagccccgcggcagcgacatcgccggcaccacaagc
accctgcaggagcagatcgcctggatgaccagcaacccccccatccccgtgggcgacatc
tacaagcgctggatcatcctgggcctgaacaagatcgtgcgcatgtacagccccgtgagc
atcctggacatcaagcagggccccaaggagcccttccgcgactacgtggaccgcttcttc
aagaccctgcgcgccgagcaggccacccaggaggtgaagaactggatgaccgacaccctg
ctggtgcagaacgccaaccccgactgcaagaccatcctgaaggccctgggccccggcgcc
accctggaggagatgatgaccgcctgccagggcgtgggcggccccagccacaaggcccgc
gtgctggccgaggccatgagccagaccaacagcgtgaacatcctgatgcagaagagcaac
ttcaagggcaacaagcgcatggtgaagtgcttcaactgcggcaaggagggccacatcgcc
cgcaactgccgcgccccccgcaagaagggctgctggaagtgcggcaaggagggccaccag
atgaaggactgcaccgagcgccaggccaacttcctgggcaagatctggcccagccacaag
ggccgccccggcaacttcctgcagaaccgccccgagcccaccgccccccccgccgagagc
ttccgcttcgaggagaccacccccgcccccaagcaggagagcaaggaccgcgaggccctg
accagcctgaagagcctgttcggcagcgaccccctgagccagtaa
5' End
3' End
Notes
Expression VectorpcDNA 3.1pcDNA3.1
Assay Methodsautoradiography, western blot, ELISpot, ELISAautoradiography, western blot, ELISpot, ELISA
Resultsundetectable.Significant increased
Protein FunctionDNA binding ( GO:0003677 ), RNA binding ( GO: 0003723), RNA-directed DNA polymerase activity ( GO: 0003964)
Recoding PurposeTo improve expression
Synthesized ByAuthors
Recoding MethodThe codon usage of the major 96ZM651.8 gene sequences was transcribed manually to that of highly
expressed human genes by changing third-codon positions from A or T to G or C residues respectively.
Publication Author(s)Gao, F.; Li, Y.; Decker, J. M.; Peyerl, F. W.; Bibollet-Ruche, F.; Rodenburg, C. M.; Chen, Y.; Shaw, D. R.; Allen, S.; Musonda, R.; Shaw, G. M.; Zajac, A. J.; Letvin, N.; Hahn, B. H.
Corresponding AuthorBeatrice H. Hahn
Corresponding AddressDepartment of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.
Publication Year2003
Publication TitleCodon usage optimization of HIV type 1 subtype C gag, pol, env, and nef genes: in vitro expression and immune responses in DNA-vaccinated mice
AbstractCodon usage optimization of human immunodeficiency virus type 1 (HIV-1) structural genes has been shown to increase protein expression in vitro as well as in the context of DNA vaccines in vivo; however, all optimized genes reported thus far are derived from HIV-1 (group M) subtype B viruses. Here, we report the generation and biological characterization of codon usage-optimized gag, pol, env (gp160, gp140, gp120), and nef genes from a primary (nonrecombinant) HIV-1 subtype C isolate. After transfection into 293T cells, optimized subtype C genes expressed one to two orders of magnitude more protein (as determined by immunoblot densitometry) than the corresponding wild-type constructs. This effect was most pronounced for gp160, gp140, Gag, and Pol (>250-fold), but was also observed for gp120 and Nef (45- and 20-fold, respectively). Optimized gp160- and gp140-derived glycoproteins were processed, incorporated into virus particles, and mediated virus entry when expressed in trans to complement an env-minus HIV-1 provirus. Mice immunized with optimized gp140 DNA developed antibody as well as CD4+ and CD8+ T cell immune responses that were orders of magnitude greater than those of mice immunized with wild-type gp140 DNA. These data confirm and extend previous studies of codon usage optimization of HIV-1 genes to the most prevalent group M subtype. Our panel of matched optimized and wild-type subtype C genes should prove valuable for studies of protein expression and function, the generation of subtype-specific immunological reagents, and the production of DNA-based sub-unit vaccines directed against a broader spectrum of viruses.
JournalAIDS Res Hum Retroviruses. 19(9): 817-23.
SummaryThe authors reported the generation and biological characterization of codon usage-optimized gag, pol, env (gp160, gp140, gp120), and nef genes from a primary HIV1 subtype C isolate. The codon usage of the major 96ZM651.8 gene sequences was transcribed manually to that of highly expressed human genes by changing third-codon positions from A or T to G or C residues respectively. None of these substitutions resulted in changes of the encoded protein sequences. Experiments were done both in vitro and vivo for the expression levels and for cellular immune responses. The experimental results showed that the codon optimized genes increased the expression levels as well as cellular immune responses.
Comments
Discussion http://www.evolvingcode.net/forum/viewtopic.php?t=660
PubMed ID14585212
Submitter NameZin, Htar
Submitter Address1000 Hilltop Circle, Baltimore, MD 21250
Entry ConfirmationNo
 
 

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