This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
LDLR Gene Homology
Homologs to the human LDLR gene were established using HomoloGene. BLAST was then utilized in order to compare similarity between the full length human LDLR gene and each homologous full length gene. BLAST was also performed on the mRNA sequences. Megablast, a BLAST algorithm that recognizes only the most similar sequences, was used for all species except Danio rerio. Danio rerio did not show any similarity with human LDLR with megablast, therefore the less stringent blastn algorithm was used in order to obtain the E-value. A low
E-value corresponds to a high level of sequence similarity.
E-value corresponds to a high level of sequence similarity.
Pan troglodytes (Chimpanzee)--LDLR
Gene Accession Number--NC_006486.2
DNA Length--45374 base pairs
E-value--0.0
mRNA Accession Number--XM_001167447.1 (transcript variant 7)
mRNA Length--5264 base pairs
E-value--0.0
Bos taurus (Cow)--LDLR
Gene Accession Number--NC_007305.3
DNA Length--33668 base pairs
E-value--7e-116
mRNA Accession Number--XM_868927.2
mRNA Length--4359 base pairs
E-value--0.0
Mus musculus (Mouse)--Ldlr
Gene Accession Number--NC_000075.5
DNA Length--26326 base pairs
E-value--2e-45
mRNA Accession Number--NM_010700.2
mRNA Length--4531 base pairs
E-value--0.0
Rattus norvegicus (Rat)--Ldlr
Gene Accession Number--NC_005107.2
DNA Length--22881 base pairs
E-value--4e-37
mRNA Accession Number--NM_175762.2
mRNA Length--3037 base pairs
E-value--0.0
Danio rerio (Zebrafish)--ldlr
Gene Accession Number--NC_007114.3
DNA Length--22096 base pairs
E-value--2e-22
mRNA Accession Number--NM_001030283.1
mRNA Length--2736 base pairs
E-value--2e-116
Gene Accession Number--NC_006486.2
DNA Length--45374 base pairs
E-value--0.0
mRNA Accession Number--XM_001167447.1 (transcript variant 7)
mRNA Length--5264 base pairs
E-value--0.0
Bos taurus (Cow)--LDLR
Gene Accession Number--NC_007305.3
DNA Length--33668 base pairs
E-value--7e-116
mRNA Accession Number--XM_868927.2
mRNA Length--4359 base pairs
E-value--0.0
Mus musculus (Mouse)--Ldlr
Gene Accession Number--NC_000075.5
DNA Length--26326 base pairs
E-value--2e-45
mRNA Accession Number--NM_010700.2
mRNA Length--4531 base pairs
E-value--0.0
Rattus norvegicus (Rat)--Ldlr
Gene Accession Number--NC_005107.2
DNA Length--22881 base pairs
E-value--4e-37
mRNA Accession Number--NM_175762.2
mRNA Length--3037 base pairs
E-value--0.0
Danio rerio (Zebrafish)--ldlr
Gene Accession Number--NC_007114.3
DNA Length--22096 base pairs
E-value--2e-22
mRNA Accession Number--NM_001030283.1
mRNA Length--2736 base pairs
E-value--2e-116
Analysis
The general trend for sequence similarity seems to be related to sequence length. The human LDLR gene is 44450 base pairs and its mRNA is 5265 base pairs. It can be seen that the closer the homologous gene is in length to the human gene, the more similar they are. Pan troglodytes, Homo sapiens closest animal relative, has an LDLR gene very similar to the Homo sapiens gene, and this sequence similarity is reflected in the similar sequence length. Also, it seems that as the LDLR gene has evolved it has been gaining base pairs. This can be seen by comparing sequence length of the most divergent homolog, Dan rerio, to Homo sapiens. However, the number of amino acids in the protein has remained relatively stable across all homologs (See Protein Homology).
