Skip to main content

Advertisement

Table 2 PPRE prediction in Gallus gallus HMGCS2, CPT1A and ACOX1 genomic DNA sequences

From: Transcriptome profiling of the feeding-to-fasting transition in chicken liver

Genes Species Ensembl ID PPRE Pattern Location Strand Methods
HMGCS2 RNO Rodriguez et al . 1994[79] GGGCCAaAGGTCT Promoter region   
  GGA ENSGALG00000002960 GGGCCAaAGGTCC -530 + STAN/PATSER
  HSA ENSG00000134240 GGGTCAaAGGGCT -118 + STAN
  MUS ENSMUSG00000027875 GGGCCAaAGGGAT -104 RC STAN
CPT1A HSA/MUS/RNO Napal et al ., 2005[80] AGGGGAaAGGTCA Intronic region between exon 1 and exon 2
  GGA ENSGALG00000007077 AGGGAAaAGGGCA 4964 + STAN
  HSA ENSG00000110090 AGGGGAaAGGTCA 2426 + STAN
  MUS ENSMUSG00000024900 AGGGGAaAGGTTA 2180 RC STAN
ACOX1 MUS Tugwood et al ., 1992[81] AGGACAaAGGTCA Promoter region   
  GGA ENSGALG00000002159 - - -  
  HSA ENSG00000161533 - - -  
  MUS ENSMUSG00000020777 - - -  
  RNO Krey et al ., 1995[82] AGGTAGaAGGTCA Promoter region   
  GGA ENSGALG00000002159 AGGAAGaAAGTCA -3931 + STAN/PATSER
  HSA ENSG00000161533 - - - STAN
  MUS ENSMUSG00000020777 AGGTAAaAGGTCA 52 + STAN
  1. PPRE patterns used for the research is indicated in bold with the reference associated. GGA: Gallus gallus; HSA: Homo sapiens; MUS: Mus musculus. Nucleic acids in red indicate conserved nucleic acids with the PPREs used for the research. Location: genomic location refers to the start of the Ensembl first exon (+1). Strand: "RC" indicates that the sequence is reverse complemented compared to the genomic sequence displayed at that location, otherwise a "+" is indicated. STAN or PASTER indicates that the PPRE has been identified either by STAN or PATSER softwares respectively (see Methods). For the ACOX1 gene, despite previous results indicating PPRE in the Mus musculus promoting DNA sequence [81], we cannot found any PPRE with the STAN procedure in any species. We used another PPRE pattern [82] identified in the Rattus norvegicus DNA sequence. This pattern allowed us to identify potential PPRE in Gallus gallus and Mus musculus sequences. The absence of result in the Homo sapiens sequence was consistent with the literature [78].