This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Homology
The homologs of KRAS is obtained using Homologene[1]. Up to 11 homologs of KRAS was found, of which 5 is included here.. For ease of comparison, the human KRAS gene and protein will be listed first before the other homologs.
Homo sapiens (Humans)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS)
Gene accession number:NC_000012.11
Protein accession number: NP_004976.2
Pan troglodytes (Chimpanzee)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_006479.2
Protein accession number: NP_004976.2
Mus musculus (Mouse)
Gene name: Kras v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_000072.5
Protein accession number: NP_067259.3
Bos taurus (Cow)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_007303.4
Protein accession number: NP_001103471.1
Canis lupus familiaris (Dog)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_006600.2
Protein accession number: XP_540523.2
Caenorhabditis elegans (Roundworm)
Gene name: let-60 LEThal
Gene accession number: NC_003282.6
Protein accession number: NP_502213.3
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS)
Gene accession number:NC_000012.11
Protein accession number: NP_004976.2
Pan troglodytes (Chimpanzee)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_006479.2
Protein accession number: NP_004976.2
Mus musculus (Mouse)
Gene name: Kras v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_000072.5
Protein accession number: NP_067259.3
Bos taurus (Cow)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_007303.4
Protein accession number: NP_001103471.1
Canis lupus familiaris (Dog)
Gene name: v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
Gene accession number: NC_006600.2
Protein accession number: XP_540523.2
Caenorhabditis elegans (Roundworm)
Gene name: let-60 LEThal
Gene accession number: NC_003282.6
Protein accession number: NP_502213.3
FASTA text file of DNA homologs
| fasta_-_dna.txt |
The above figure was obtained from TreeFam[2].
Boxes correspond to Pfam domains, while lines to non-domain regions. Dark lines or boxes show matched parts, while light ones gaps. Vertical dark blue lines indicate splicing boundaries. [2]
Boxes correspond to Pfam domains, while lines to non-domain regions. Dark lines or boxes show matched parts, while light ones gaps. Vertical dark blue lines indicate splicing boundaries. [2]
Gene Tree
The above gene tree was obtained from emsembl [3].
Alignment
This alignment analysis of the gene of the homologs was obtained using T-coffee [4]. However, due to the limits of the T-coffee online program, almost all of the homologous genes had to be truncated (except C.elegens). Thus, it is likely that the results could be unexpected.
| alignment-dna.pdf |
Analysis
The results from T-coffee and TreeFam vary greatly. In T-coffee, the alignment is described as bad or weak, however in the TreeFam figure above, we can clearly see a high degree of alignment. This is probably because during input of the FASTA sequences into the T-coffee program, most of the homologous genes had to be severely truncated due to the limitations of the program. Since I did this by using roughly the first 1000 of the nucleotides, it is likely that in many of the genes analyzed, the coding sequence is not among the first 1000 nucleotides, in other words, the conserved sequences might not be included in the input of the T-coffee program. Therefore, it is likely that TreeFam has a more accurate portrayal of the alignment of the homologues analyzed.
References
1) Homologene
http://www.ncbi.nlm.nih.gov/homologene
2) TreeFam
http://www.treefam.org/
3. Ensembl
http://uswest.ensembl.org
3) T-coffee
http://www.ebi.ac.uk/Tools/msa/tcoffee/
http://www.ncbi.nlm.nih.gov/homologene
2) TreeFam
http://www.treefam.org/
3. Ensembl
http://uswest.ensembl.org
3) T-coffee
http://www.ebi.ac.uk/Tools/msa/tcoffee/
