Part:BBa_K3952001

APOB-100 (Cholesterol Deficiency Allele)

Located within chromosome 11 of the Bos taurus genome, the APOB gene codes for apolipoprotein B, a protein involved in the transport of cholesterol in the bloodstream. Studies have reported an inheritable allele within the APOB gene that causes cholesterol deficiency (CD) in cattle. This part contains the cholesterol deficiency allele in the APOB gene with a transposable insertion between nucleotides CT at positions 221, 222. Part: BBa_K3952000 is the wild-type version of the APOB gene that contains nucleotides CT at positions 221, 222.

The APOB gene (Gene ID 494004) was located within the genomic DNA sequence of the Bos taurus, using the NCBI reference assembly.

Usage and Biology

The purpose of this part is to serve as a negative control for a Flappase genetic testing system. Therefore the sequence provide is only a fragment of the Bos taurus genome. The sequence was cut in order to only showcase where the allele would be present (exon 5), in addition to the ease of cloning a smaller sequence would provide.

This part does contain the APOB inheritable allele. The allele is created by an insertion of a transposable element (also known as the jumping gene or ERV2-1) into the APOB gene. The insertion occurs between the 24th and 25th nucleotide of exon 5. The insertion polymorphism is approximately 300 bp. The resulting polymorphism is cholesterol deficiency (CD).

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 330
  Illegal XhoI site found at 591
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal SapI.rc site found at 853