Nucleotide sequence of a human gene for glutathione peroxidase

AbstractThe capacity of the scientific literature to self-correct is of vital importance, but few studies have compared post-publication journal responses to specific error types. We have compared journal responses to a specific reagent error in 31 human gene knockdown publications, namely a non-targeting or negative control nucleotide sequence that is instead predicted to target a human gene. The 31 papers published by 13 biomedical journals generated 26 published responses (14 retractions, 5 expressions of concern, 7 author corrections which included one resolved expression of concern) as well as 6 stated decisions to take no action. Variations in published responses were noted both between journals and by 4 journals that published different responses to at least 2 papers. A subset of published responses revealed conflicting explanations for the wrongly identified control reagent, despite 30/31 papers obtaining their gene knockdown reagents from the same external supplier. Viewed collectively, different journal responses to human gene knockdown publications with a common reagent error type suggest that editorial staff require more support to interpret post-publication notifications of incorrect nucleotide sequence reagents. We propose a draft template to facilitate the communication, interpretation and investigation of published errors, including errors affecting research reagents.

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Identification of human gene research articles with wrongly identified nucleotide sequences

Life Science Alliance ◽

10.26508/lsa.202101203 ◽

2022 ◽

Vol 5 (4) ◽

pp. e202101203

Author(s):

Yasunori Park ◽

Rachael A West ◽

Pranujan Pathmendra ◽

Bertrand Favier ◽

Thomas Stoeger ◽

...

Keyword(s):

Nucleotide Sequence ◽

Screening Tool ◽

Human Gene ◽

Molecular Techniques ◽

Research Articles ◽

Protein Coding ◽

Human Research ◽

Protein Coding Genes ◽

Non Coding Rnas ◽

Automated Screening

Nucleotide sequence reagents underpin molecular techniques that have been applied across hundreds of thousands of publications. We have previously reported wrongly identified nucleotide sequence reagents in human research publications and described a semi-automated screening tool Seek & Blastn to fact-check their claimed status. We applied Seek & Blastn to screen >11,700 publications across five literature corpora, including all original publications in Gene from 2007 to 2018 and all original open-access publications in Oncology Reports from 2014 to 2018. After manually checking Seek & Blastn outputs for >3,400 human research articles, we identified 712 articles across 78 journals that described at least one wrongly identified nucleotide sequence. Verifying the claimed identities of >13,700 sequences highlighted 1,535 wrongly identified sequences, most of which were claimed targeting reagents for the analysis of 365 human protein-coding genes and 120 non-coding RNAs. The 712 problematic articles have received >17,000 citations, including citations by human clinical trials. Given our estimate that approximately one-quarter of problematic articles may misinform the future development of human therapies, urgent measures are required to address unreliable gene research articles.

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Nucleotide sequence of c-H-ras-1 gene from B6C3F1 mice.

Acta Biochimica Polonica ◽

10.18388/abp.1996_4493 ◽

1996 ◽

Vol 43 (3) ◽

pp. 575-578 ◽

Cited By ~ 3

Author(s):

B Przybojewska ◽

G Płucienniczak

Keyword(s):

Amino Acids ◽

Nucleotide Sequence ◽

Protein Sequence ◽

Human Gene ◽

Ras Gene ◽

Nucleotide Level ◽

B6c3f1 Mouse ◽

B6c3f1 Mice ◽

High Degree

The c-H-ras-1 gene of an B6C3F1 mouse was isolated and nucleotide sequence determined. Our study has revealed that this c-H-ras-1 gene consists of four exons, separated by three introns ranging in size from 150 to 649 bp. The coding parts of the sequence of mouse c-H-ras-1 gene show no important differences as compared with those of the rat, hamster and human gene. More numerous changes were found in introns. The identity of mouse c-H-ras-1 gene with rat, hamster and human ones at the nucleotide level is 86.40%, 80.04% and 67.87%, respectively. Comparison of amino acids in protein sequence of c-H-ras gene of mouse, rat, hamster and human points to high degree of conservation of the gene.

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Nucleotide sequence of cDNA for rabbit glutathione peroxidase

Nucleic Acids Research ◽

10.1093/nar/17.5.2136 ◽

1989 ◽

Vol 17 (5) ◽

pp. 2136-2136 ◽

Cited By ~ 14

Author(s):

Masami Akasaka ◽

Junzo Mizoguch ◽

Shinichi Yoshimura ◽

Keiichi Watanabe

Keyword(s):

Nucleotide Sequence ◽

Glutathione Peroxidase

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Human gene encoding CD38 (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase): organization, nucleotide sequence and alternative splicing

Gene ◽

10.1016/s0378-1119(96)00723-8 ◽

1997 ◽

Vol 186 (2) ◽

pp. 285-292 ◽

Cited By ~ 52

Author(s):

Koji Nata ◽

Toshinari Takamura ◽

Tadahiro Karasawa ◽

Tomoko Kumagai ◽

Wataru Hashioka ◽

...

Keyword(s):

Alternative Splicing ◽

Nucleotide Sequence ◽

Human Gene ◽

Gene Encoding ◽

Adp Ribosyl Cyclase ◽

Cyclic Adp Ribose

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Nucleotide sequence of a rat glutathione peroxidase cDNA

Nucleic Acids Research ◽

10.1093/nar/16.11.5207 ◽

1988 ◽

Vol 16 (11) ◽

pp. 5207-5207 ◽

Cited By ~ 39

Author(s):

Ye-Shih Ho ◽

Adriann J. Howard ◽

James D. Crapo

Keyword(s):

Nucleotide Sequence ◽

Glutathione Peroxidase

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Genomic cloning, complete nucleotide sequence, and structure of the human gene encoding the major intrinsic protein (MIP) of the lens

Genomics ◽

10.1016/0888-7543(91)90023-8 ◽

1991 ◽

Vol 11 (4) ◽

pp. 981-990 ◽

Cited By ~ 36

Author(s):

M. Michele Pisano ◽

Ana B. Chepelinsky

Keyword(s):

Nucleotide Sequence ◽

Complete Nucleotide Sequence ◽

Human Gene ◽

Major Intrinsic Protein ◽

Gene Encoding ◽

Intrinsic Protein ◽

Genomic Cloning

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Nucleotide sequence of the 3' portion of a human gene for protein kinase CβI/βII

Nucleic Acids Research ◽

10.1093/nar/15.17.7179 ◽

1987 ◽

Vol 15 (17) ◽

pp. 7179-7180 ◽

Cited By ~ 18

Author(s):

Kyoto Kubo ◽

Shigeo Ohno ◽

Koichi Suzuki

Keyword(s):

Protein Kinase ◽

Nucleotide Sequence ◽

Human Gene

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Genetic analysis of SARS-CoV-2 and the common golden nucleotides to human gene

10.21203/rs.3.rs-854956/v1 ◽

2021 ◽

Author(s):

Hamed Babaee

Keyword(s):

Dna Replication ◽

Nucleotide Sequence ◽

Genetic Analysis ◽

Human Genome ◽

Human Gene ◽

Human Genes ◽

Reference Virus ◽

The Common ◽

Disease Factor

Abstract BackgroundThe coronavirus disease pandemic began in 2019 in Wuhan, China, and continues into 2021, as new mutant viruses appear and require new solutions and treatments. Methods and ResultsIn this study, by genetic analysis of data from 24 SARS-CoV-2 samples from different countries and their alignment with each other and the Wuhan reference virus as well as the human genome, the disease factor is looked at from another angle. The result is the identification of genetic differences in viruses, and the finding of a unique 17-nucleotide sequence between human genes, viruses, and enzymes that can contribute to the onset and progression of the disease. ConclusionsThe role of this sequence in DNA replication and the production of new proteins and its alignment with the EPPK1 gene that may cause disease and its various symptoms are likely.

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