Difference between revisions of "Part:BBa K3952001"

 
Line 3: Line 3:
 
<partinfo>BBa_K3952001 short</partinfo>
 
<partinfo>BBa_K3952001 short</partinfo>
  
−
Located between exon 29 chromosome 11, apolipoprotein B (APOB) is a 1300bp insertion of a transposable LTR element (ERV2-1). This SNP results in a cholesterol deficiency in Bos taurus. The purpose of this part is to serve as a new target for an SNP detection system.  
+
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. Using the NCBI reference assembly, the APOB gene (Gene ID 494004) was located within the genomic DNA sequence of the Bos taurus. Studies have reported an inheritable allele within the APOB gene that causes cholesterol deficiency in cattle. This part contains the mutant-type APOB gene, meaning the allele is present.
  
−
<!-- Add more about the biology of this part here
+
<!-- -->
 
===Usage and Biology===
 
===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).
 +
 +
  
 
<!-- -->
 
<!-- -->

Revision as of 15:55, 18 October 2021


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. Using the NCBI reference assembly, the APOB gene (Gene ID 494004) was located within the genomic DNA sequence of the Bos taurus. Studies have reported an inheritable allele within the APOB gene that causes cholesterol deficiency in cattle. This part contains the mutant-type APOB gene, meaning the allele is present.

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