Primary structure of ovine tumor necrosis factor alpha cDNA

Young, Adamo; Hay, J. B.; Chan, John

doi:10.1093/nar/18.22.6723

Cited by 16 publications

(1 citation statement)

References 6 publications

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“…In sheep, there is little information about polymorphism of the TNF gene. In the 1990s, ovine TNF was cloned by three different groups (Young et al ., 1990; Green & Sargan, 1991; Nahs et al ., 1991). Two of the three cDNAs cloned were identical and the third one lacked an amino acid in the leader sequence.…”

Section: Introductionmentioning

confidence: 99%

Detection of polymorphisms in the tumour necrosis factor alpha candidate gene in sheep

Álvarez-Busto¹,

Ruiz²,

Mazon³

et al. 2004

European Journal of Immunogenetics

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Primers based on GenBank sequences of the ovine tumour necrosis factor (TNF)-alpha gene were designed to amplify a 273-bp fragment comprising part of the fourth exon and the 3' untranslated region (UTR) of the ovine TNF-alpha gene. Five different single-strand conformational polymorphism (SSCP) patterns were detected in a number of unrelated animals and three different alleles were identified and sequenced. These alleles differed in one deletion and one single nucleotide polymorphism (SNP) and were named TNF*01, TNF*02 and TNF*03. These alleles corresponded to three sequences previously characterized by other groups. In the population analysis, no significant differences were found in the frequencies of the Latxa and Rasa breeds. This is the first description of allelic variation in the ovine TNF-alpha gene.

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Section: Introductionmentioning

confidence: 99%

Detection of polymorphisms in the tumour necrosis factor alpha candidate gene in sheep

Álvarez-Busto¹,

Ruiz²,

Mazon³

et al. 2004

European Journal of Immunogenetics

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Interpreting cDNA sequences: Some insights from studies on translation

1996

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This review discusses some rules for assessing the completeness of a cDNA sequence and identifying the start site for translation. Features commonly invoked-such as an ATG codon in a favorable context for initiation, or the presence of an upstream in-frame terminator codon, or the prediction of a signal peptide-like sequence at the amino terminus-have some validity; but examples drawn from the literature illustrate limitations to each of these criteria. The best advice is to inspect a cDNA sequence not only for these positive features but also for the absence of certain negative indicators. Three specific warning signs are discussed and documented: (i) The presence of numerous ATG codons upstream from the presumptive start site for translation often indicates an aberration (sometimes a retained intron) at the 5' end of the cDNA. (ii) Even one strong, upstream, out-of-frame ATG codon poses a problem if the reading frame set by the upstream ATG overlaps the presumptive start of the major open reading frame. Many cDNAs that display this arrangement turn out to be incomplete; that is, the out-of-frame ATG codon is within, rather than upstream from, the protein coding domain. (iii) A very weak context at the putative start site for translation often means that the cDNA lacks the authentic initiator codon. In addition to presenting some criteria that may aid in recognizing incomplete cDNA sequences, the review includes some advice for using in vitro translation systems for the expression of cDNAs. Some unresolved questions about translational regulation are discussed by way of illustrating the importance of verifying mRNA structures before making deductions about translation.

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