This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
NOTCH1 DNA homology and alignment
NOTCH1 homologs were obtained via searches in nBLAST, TreeFam, Ensembl, and FlyBase. As in the Protein homology and alignment page, analysis will only be carried out on the first few organisms (in blue). In comparison with the protein homology page, the analysis for Macaca mulatta and Cynops pyrrhogaster have been dropped due to the difficulty in obtaining the corresponding gene sequences.
NOTCH1 homologs were obtained via searches in nBLAST, TreeFam, Ensembl, and FlyBase. As in the Protein homology and alignment page, analysis will only be carried out on the first few organisms (in blue). In comparison with the protein homology page, the analysis for Macaca mulatta and Cynops pyrrhogaster have been dropped due to the difficulty in obtaining the corresponding gene sequences.
Pan troglodytes
Gene symbol: NOTCH1 Gene accession number: NC_006476.3 Gene ID: 464865 Ensembl ID: ENSPTRG00000021561 Mus musculus
Gene symbol: Notch1 Gene accession number: NC_000068.6 Gene ID: 18128 Ensembl ID: ENSMUSG00000026923 Rattus norvegicus
Gene symbol: Notch1 Gene accession number: NC_005102.2 Gene ID: 25496 Ensembl ID: ENSRNOG00000019322 Canis lupus
Gene symbol: NOTCH1 Gene accession number: NC_006591.3 Gene ID: 480676 Enseml ID: ENSCAFG00000019633 |
Danio rerio
Gene symbol: notch1a Gene accession number: NC_007132.5 Gene ID: 30718 Ensembl ID: ENSDARG00000044841 Gallus gallus
Gene symbol: NOTCH1 Gene accession number: NC_006104.3 Gene ID: 395655 Ensembl ID: ENSGALG00000002375 Drosophila melanogaster
Gene symbol: N Gene accession number: NC_004354.3 Gene ID: 31293 FlyBase ID: FBgn0004647 |
The document below contains DNA sequences (in FASTA format) of human NOTCH1 and its putative homologs, which have been limited to the first ~2000 nucleotides after eliminating any long sequences of unknown nucleotides:
gene_homologs.txt | |
File Size: | 14 kb |
File Type: | txt |
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Apart from the alignments above, the following alignment (obtained directly from Ensembl) shows the comparison of human NOTCH1 gene with 10 other eutherian mammals:
ClustalW alignment | |
File Size: | 1633 kb |
File Type: | alignment |
Analysis
The DNA sequences analyzed in this page correspond to the protein homologs presented in the Protein homology and alignment page. When the entire NOTCH1 DNA sequence was used to perform nBLAST search in discontiguous megablast, two error messages were displayed indicating that there were too many high-scoring segment pairs (HSPs) and that CPU usage limit was exceeded. Although results were obtained when the setting was changed to megablast, majority of the hits obtained were mRNA sequences instead of DNA. Hence, TreeFam, Ensembl and FlyBase were used for additional searches to generate the results above. For DNA sequence alignment, all of the DNA sequences had to be severely truncated because the gene sizes for NOTCH1 and its putative homologs are too large to fit the size limitation of the analysis programs. As a result, it is not surprising that the alignment results were very poor. Protein analysis is therefore a better reflection of Notch1 homology.
References:
- Dereeper A., Audic S., Claverie J.M., Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010 Jan 12;10:8. (PubMed)
- Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
- Notredame C., Higgins DG., Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000, Sep 8;302(1):205-17. (PubMed)