This web page was produced as an assignment for Genetics 677, an undergraduate course at UW‐Madison.
Homologous BLM gene
Homologs of BLM gene can be found on Homologene. The following file is a compilation of DNA sequences (in FASTA format) of 9 BLM gene homologs. BLM gene is conserved in chimpanzee, cow, mouse, rat, chicken, zebrafish, A.thaliana, rice, and P.falciparum [1].
homolog_DNA_sequence.doc | |
File Size: | 41 kb |
File Type: | doc |
List of BLM gene homologs:
Pan troglodytes (Chimpanzee)
Gene name: BLM Gene accession number: NC_006482.2 Protein accession number: XP_510594.2 Bos taurus (Cattle) Gene name: BLM Gene accession number:NC_007319.4 Protein accession number: XP_613809.3 Mus musculus (Mouse) Gene name: Blm Gene accession number: NC_000073.5 Protein accession number: NP_001035992.1 Gallus gallus (Chicken) Gene name: BLM Gene accession number:NC_006097.2 Protein accession number: NP_001007088.1 Danio rerio (Zebrafish) Gene name:blm Gene accession number: NC_007129.4 Protein accession number: XP_701357.3 |
Arabidopsis thaliana (thale cress)
Gene name: RECQI1 Gene accession number:NC_003074.8 Protein accession number:NP_187225.2 Oryza sativa Japonica Group (rice) Gene name: Os11g0672700 Gene accession number:NC_008404.2 Protein accession number: NP_001068436.1 Plasmodium falciparum 3D7 (Laverania) Gene name: PFI0910w Gene accession number:NC_004330.1 Protein accession number: XP_001352057.1 Rattus norvegicus (Rat) Gene name:Blm Gene accession number:NC_005100.2 |
Alignments
t-coffee_DNA_alignment.pdf | |
File Size: | 401 kb |
File Type: |
clustal_2_DNA_alignment.doc | |
File Size: | 52 kb |
File Type: | doc |
Analysis
Since the gene sequences for human and the 9 homologs are too long to be processed by most of the databases, I had to truncate the number of nucleotides in each species to around 1050 nucleotides. I had no trouble aligning the gene sequences using T-Coffee 6.85,, and in fact the results generated by T-Coffee is helpful because the color labeling eases interpretation of the results. The results from T-Coffee suggested that the gene alignment are pretty bad and most of the sequences are not well-conserved. The fact that I truncated the sequences to only 1050 nucleotides might have biased the results. By using ClustalW 2.0.3, I received an error message that said "detected leading and trailing spaces in sequence #6 (Zebrafish) and #9(Laverania) were removed". However, ClustralW yielded the same result as T-Coffee
References
1) Homologene: http://www.ncbi.nlm.nih.gov/homologene
2) ClustalW:http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_
3) T-COFFEE: http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_type=tcoffee
2) ClustalW:http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_
3) T-COFFEE: http://www.phylogeny.fr/version2_cgi/one_task.cgi?task_type=tcoffee