Exploring the tomato Solyc03g114600.3 gene
The phytopathogenic fungus Alternaria alternata f. sp. lycopersici (AAL) produces toxins that are essential for pathogenicity of the fungus on tomato (Solanum lycopersicum). AAL toxins and fumonisins of the unrelated fungus Fusarium moniliforme are sphinganine-analog mycotoxins (SAMs), which cause inhibition of sphingolipid biosynthesis in vitro and are toxic for some plant species and mammalian cell lines. SAM resistance of tomato is determined by the ASC-1 gene. (See also: Brandwagt et al. A longevity assurance gene homolog of tomato mediates resistance to Alternaria alternata f. sp. lycopersici toxins and fumonisin B1. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4961-6).
(a) Find the tomato Solyc03g114600.3 gene. On which chromosome and which strand of the genome is this gene located?
(b) How long is its transcript? How long is the protein it encodes? How many exons does it have? Are any of the exons completely or partially untranslated?
(c) Have a look at the external references for the transcript. What can you find out about the Solyc03g114600.3 protein?
(d) Where in the cell is the Solyc03g114600.3 protein located? Does the protein contain any transmembrane domains?
(e) Export the sequence of the gene, transcript and protein in FASTA format.
(a) Go to the Ensembl Plants homepage. Select Solanum lycopersicum from the species list and type Solyc03g114600.3 in the search box. Click Go. Click on Solyc03g114600.3.
The tomato Solyc03g114600.3 gene is located on chromosome 3 on the reverse strand.
(b) Click on Show transcript table.
The length of its transcript is 4316 base pairs and the length of the encoded protein is 308 amino acids.
Click on the Ensembl Transcript ID Solyc03g114600.3.1 in the transcript table.
It has six exons.
Click on Sequence - Exons in the side menu.
The first and last exons are partially untranslated (sequence shown in orange). This can also be seen from the fact that in the transcript diagrams on the Gene summary and Transcript summary pages the boxes representing the first and last exon are partially unfilled and narrower.
(c) Click on General identifiers in the side menu. Explore some of the links (a good place to start is usually UniProtKB/Swiss-Prot).
(d) Go back to the gene tab then click on GO: cellular component in the side menu.
The protein is located in the membrane of the endoplasmic reticulum.
Return to the transcript tab and click on Protein summary or Domains & features in the side menu.
The protein does contain five transmembrane domains.
(e) Click on the blue Export data button. Under Options for FASTA sequence, select Genomic: Unmasked, cDNA and Peptide sequence. Click Next>. Click on Text.
This returns three sequences (one gene, one transcript and one protein sequence):
>Solyc03g114600.2:Solyc03g114600.2.1 cdna:KNOWN_protein_coding
AACAATTCGAAAACTTGTTCTGCAATTCATTTGAAACTACAACAATAGAAGAAGAAAAAA
AAAGTTCAATTCAACAGATTTTTGAAAAAAAAAGTCAACAGATGAAAAACCTGGATCACA
TCGCTGCTTCGGTTGATTGGGAGAAAGAGTCTCTCCCTGAGTACCAGGATTTGATATTTC
etc.
>Solyc03g114600.2:Solyc03g114600.2.1 peptide: Solyc03g114600.2.1 pep:KNOWN_protein_coding
MKNLDHIAASVDWEKESLPEYQDLIFLLFFALFFPVLRFILDRFVFEALAKRMIFGKKTV
VNINGREERKKINKFKESAWKFVYFLSTELLALSVTCNEPWFTDSRYFWAGPGDVVWPNL
KMKLKLKLLYMYAGGFYFYSIFATLYWETRRYDFAAQIIHHVTTVSLIVLSYVYGFARIG
etc.
>3 dna:chromosome chromosome:SL2.40:3:58592692:58594435:-1
AACAATTCGAAAACTTGTTCTGCAATTCATTTGAAACTACAACAATAGAAGAAGAAAAAA
AAAGTTCAATTCAACAGATTTTTGAAAAAAAAAGTCAACAGATGAAAAACCTGGATCACA
TCGCTGCTTCGGTTGATTGGGAGAAAGAGTCTCTCCCTGAGTACCAGGATTTGATATTTC
etc.
