Sequence and function analysis of fugu cosmid sequence
Pufferfish, often known as fugu, or Japanese fugu, or river pig, belongs to the Takifugu genus.
There are 25 species in this genus found in salt or fresh water. Genome sequencing of the species
of Takifugu rubripes (Dong Fang Hong Qi Tun) was initiated by Sydney Brenner and his colleagues
in 1989. The small genome size (~400MB) and similar number of genes make it a good model for
comparative genomics. The fugu genome sequence is available at the ENSEMBL genome database
Fugu Genome.
In 1998, Liu et al. obtained a fugu cosmid sequence of 39757bp
(GenBank Accession: AF164138).
Five genes were identified with bioinformatics tools in this cosmid: two tandem multidrug
resistance (MDR) genes at the 5' followed by three enzymes,
(Carnitine octanoyltransferase, RNase P38, and N-myristoyltransferase 2). We use this cosmid
sequence as an example for genomic sequence analysis.
Exercises
- Find the fugu cosmid sequence entry from NCBI nucleotide with Accession
AF164138
and save as GenBank (AF164138_GB.txt and FASTA (AF164138.FASTA) format .
- Find the repeat fragment within AF164138.FASTA using dottup in mEMBOSS.
- Retrieve the first fragment (1-13000bp)
AF164138_F1.FAS
and second fragment (13501-25000bp)
AF164138_F2.FAS
of the cosmid sequence using
using seqret in mEMBOSS, set starting (begin) and ending (end) with Input Sequence option.
- Predict the gene structure of the first and second fragments
using FGenesh in http://www.softberry.com/berry.phtml/berry.phtml
Softberry.
select Takifugu ribripes from the Organism option list.
- Retrieve the coding sequence of two genes
FUGU_MDR2_CDS.FAS
and
FUGU_MDR3_CDS.FAS
as well as their encoded amino acid sequence
FUGU_MDR2_AA.FAS
and
FUGU_MDR3_AA.FAS
from AF164138 with coderet in mEMboss.
- Compare the sequence similarity between MDR2 and MDR3 at the DNA, mRNA and protein level.
- Check the repeat domain within MDR2 and MDR3.
- Find MDR3_HUMAN in UniProt, analyze the 3D structure with PDBSum.
- Predict the 3D structure of fugu MDR3 Q804Z6_TAKRU
References:
- TransporterDB
- The transporter database for the predicted cytoplasmic membrane transport
protein complement with complete genome sequence.
- Michael Dean, The Human ATP-Binding Cassette (ABC) Transporter Superfamily.
[NCBI Bookshelf]
- Liu Y, Cloning and analysis of Takifugu rubripes cosmid sequence.
Peking Medical University, 1998.
[PhD Thesis
| PhD Thesis Abstract]
- Xu LM, Analysis of the Fugu cosmid sequence. Homework of the ABC course (in Chinese).
[PDF]
A website for the analysis of the Fugu cosmid