Difference between revisions of "Part:BBa K3952004"

Latest revision as of 00:59, 20 October 2021

LRP4 (Syndactylous Hooves)

Located within chromosome 11 of the Bos taurus genome, the LRP4 gene codes for an LDL receptor-related protein, a protein involved in the formation of the cattle's hooves. Studies have reported an inheritable syndactylous allele of the LRP4 gene that leads to congenital syndactyl (also known as mule foot) in cattle. This part contains the wildtype LRP4 gene, which differs from the syndactylous allele due to two adjacent single nucleotide polymorphisms located within exon 33 of the gene. The wildtype LRP4 contains the nucleotides CG at positions 4863 and 4864. The syndactylous LRP4 allele (part number BBa_K3952004)contains AT at positions 4863 and 4864. The substitution results in two adjacent single-nucleotide polymorphisms.

The LRP4 gene (Gene ID 504317) was located within the genomic DNA sequence of Bos taurus, using the NCBI reference assembly.

Figure 1: Sequence variation between the normal and syndactyl alleles of LRP4. The two versions differ by two SNPs, where nucleotides CG are substituted by AT at positions 4863 and 4864.

Usage and Biology

The purpose of this part is to serve as a positive control for a Flappase genetic testing system. The system requires the amplification of DNA around the polymorphism; therefore, the sequence provided is only a fragment of the Bos taurus genome. The entire sequence of the gene was not cloned to showcase where the allele would be present (exon 33), and to facilitate ease of cloning.

This part does contain the LRP4 inheritable allele. The allele is created by a substitution where nucleotides CG in the wildtype gene sequence become nucleotides AT. The substitution occurs at positions 4863 and 4864. The polymorphism resulting causes a condition known as mule foot, which refers to the fusion or non-division of the two developed digits of the bovine foot.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 325
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K3952004 short</partinfo>
-Located within chromosome 11 of the Bos taurus genome, the LRP4 gene codes for an LDL receptor-related protein, a protein involved in the formation of the cattle's hooves. Studies have reported an inheritable syndactylous allele within the LRP4 gene that leads to congenital syndactyl (also known as mule foot) in cattle. This part contains the syndactylous allele of the LRP4 gene where a substitution of nucleotides at positions 4863 and 4864, becomes AT. Part: BBa_K3952003 is the wild-type version of the LRP4 gene and its nucleotides are CG at positions 4863 and 4864. The substitution occurring in the syndactylous allele results in two adjacent single-nucleotide polymorphisms.
+Located within chromosome 11 of the ''Bos taurus'' genome, the ''LRP4'' gene codes for an LDL receptor-related protein, a protein involved in the formation of the cattle's hooves. Studies have reported an inheritable syndactylous allele of the ''LRP4'' gene that leads to congenital syndactyl (also known as mule foot) in cattle. This part contains the wildtype ''LRP4'' gene, which differs from the syndactylous allele due to two adjacent single nucleotide polymorphisms located within exon 33 of the gene. The wildtype ''LRP4'' contains the nucleotides CG at positions 4863 and 4864. The syndactylous LRP4 allele (part number  BBa_K3952004)contains AT at positions 4863 and 4864. The substitution results in two adjacent single-nucleotide polymorphisms.
-The LRP4 gene '''(Gene ID 504317)''' was located within the genomic DNA sequence of Bos taurus, using the NCBI reference assembly.
+The ''LRP4'' gene '''(Gene ID 504317)''' was located within the genomic DNA sequence of ''Bos taurus'', using the NCBI reference assembly.
 [[Image: Team SUNY Oneonta LRP4 Visual.jpeg|500px|thumb|center|'''Figure 1:''' Sequence variation between the normal and syndactyl alleles of LRP4. The two versions differ by two SNPs, where nucleotides CG are substituted by AT at positions 4863 and 4864.]]
@@ Line 14: / Line 14: @@
 ===Usage and Biology===
-The purpose of this part is to serve as a positive control for a Flappase genetic testing system. The system requires the amplification of DNA around the polymorphism, 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 33) but also allow ease of cloning.
+The purpose of this part is to serve as a positive control for a Flappase genetic testing system. The system requires the amplification of DNA around the polymorphism; therefore, the sequence provided is only a fragment of the ''Bos taurus'' genome. The entire sequence of the gene was not cloned to showcase where the allele would be present (exon 33), and to facilitate ease of cloning.
+This part ''does'' contain the ''LRP4'' inheritable allele. The allele is created by a substitution where nucleotides CG in the wildtype gene sequence become nucleotides AT. The substitution occurs at positions 4863 and 4864. The polymorphism resulting causes a condition known as mule foot, which refers to the fusion or non-division of the two developed digits of the bovine foot.
-This part ''does'' contain the LRP4 inheritable allele. The allele is created by a substitution where nucleotides CG in the normal gene sequence become nucleotides AT. The substitution occurs at positions 4863 and 4864. The polymorphism resulting causes a condition known as mule foot, which refers to the fusion or non-division of the two developed digits of the bovine foot.