Selected article for: "downstream structure and loop stem"
Author: Woo, Patrick CY; Lau, Susanna KP; Li, Kenneth SM; Tsang, Alan KL; Yuen, Kwok-Yung
Title: Genetic relatedness of the novel human group C betacoronavirus to Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5
  • Document date: 2012_11_7
    • ID: 6c68pmem_6
    Snippet: Novel human group C betacoronavious PCY Woo et al 2 103 of NS3d in Ty-BatCoV HKU4 and Pi-BatCoV HKU5 (35%-49% amino acid identities), with a stop codon UAG present at nucleotide position 27 160, leading to premature termination. NS3e of HCoV-EMC is homologous to amino acids 116/122 to 223/227 of NS3d in Ty-BatCoV HKU4 and Pi-BatCoV HKU5 (60%-62% amino acid identities). NS3c and NS3e do not possess any TRS or internal ribosomal entry site. BLAST s.....
    Document: Novel human group C betacoronavious PCY Woo et al 2 103 of NS3d in Ty-BatCoV HKU4 and Pi-BatCoV HKU5 (35%-49% amino acid identities), with a stop codon UAG present at nucleotide position 27 160, leading to premature termination. NS3e of HCoV-EMC is homologous to amino acids 116/122 to 223/227 of NS3d in Ty-BatCoV HKU4 and Pi-BatCoV HKU5 (60%-62% amino acid identities). NS3c and NS3e do not possess any TRS or internal ribosomal entry site. BLAST search revealed no amino acid similarities between these putative non-structural proteins and other known proteins and no functional domains were identified by PFAM and Inter-ProScan. TMHMM and TMpred analyses show one and two putative transmembrane domains in NS3a (residues 9 to 29) and NS3d (residues 36 to 56 and 71 to 91), respectively. Similar to Ty-BatCoV HKU4 and Pi-BatCoV HKU5, the 3' untranslated region of the genome of HCoV-EMC contains predicted bulged stem-loop structures 16 to 76 nucleotides downstream of the N genes. Downstream to the bulged stem-loop structure, 97 to 121 nucleotides downstream of the N genes, a pseudoknot structure is present. Bootscan analysis did not show any recombination between HCoV-EMC, Ty-BatCoV HKU4 and Pi-BatCoV HKU5.

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